Well all those entries are the same as mine. All C:\ for me. If all thsese are correct and you still have issues, I'm at a loss. You could always re run MultiCFS3.exe, delete the AppData folder and cfg again.
MASTERETOSTARTUP.bat in C:\
@ECHO OFF
CLS
CALL ETOEraSwapper.bat
CD "C:\CFS3 ETO ExpansionC\global_layer"
CALL ETOGLSwapper.bat
CD "C:\CFS3 ETO ExpansionC\sounds"
CALL ETOMusicSwapper.bat
START cfs3.exe
ETOMusicSwapper.bat
@ECHO OFF
CLS
ECHO.
ECHO.
ECHO WELCOME TO THE CFS3 ETO EXPANSION MUSIC SWAPPER
ECHO.
ECHO.
ECHO.
RESENT
IF NOT EXIST "C:\CFS3 ETO ExpansionC\1945_qclocations.xml" GOTO :1945_ERA
IF NOT EXIST "C:\CFS3 ETO ExpansionC\1944_qclocations.xml" GOTO :1944_ERA
IF NOT EXIST "C:\CFS3 ETO ExpansionC\1943_qclocations.xml" GOTO :1943_ERA
IF NOT EXIST "C:\CFS3 ETO ExpansionC\bob_qclocations.xml" GOTO :BOB_ERA
IF NOT EXIST "C:\CFS3 ETO ExpansionC\1936_qclocations.xml" GOTO :1936_ERA
:1936_ERA
IF NOT EXIST bob_uimusic.wav GOTO :BOB_1936GL
IF NOT EXIST 1943_uimusic.wav GOTO :1943_1936GL
IF NOT EXIST 1944_uimusic.wav GOTO :1944_1936GL
IF NOT EXIST 1945_uimusic.wav GOTO :1945_1936GL
IF NOT EXIST 1936_uimusic.wav GOTO :END
:BOB_ERA
IF NOT EXIST 1936_uimusic.wav GOTO :1936_BOBGL
IF NOT EXIST 1943_uimusic.wav GOTO :1943_BOBGL
IF NOT EXIST 1944_uimusic.wav GOTO :1944_BOBGL
IF NOT EXIST 1945_uimusic.wav GOTO :1945_BOBGL
IF NOT EXIST bob_uimusic.wav GOTO :END
:1943_ERA
IF NOT EXIST 1936_uimusic.wav GOTO :1936_1943GL
IF NOT EXIST bob_uimusic.wav GOTO :BOB_1943GL
IF NOT EXIST 1944_uimusic.wav GOTO :1944_1943GL
IF NOT EXIST 1945_uimusic.wav GOTO :1945_1943GL
IF NOT EXIST 1943_uimusic.wav GOTO :END
:1944_ERA
IF NOT EXIST 1936_uimusic.wav GOTO :1936_1944GL
IF NOT EXIST bob_uimusic.wav GOTO :BOB_1944GL
IF NOT EXIST 1943_uimusic.wav GOTO :1943_1944GL
IF NOT EXIST 1945_uimusic.wav GOTO :1945_1944GL
IF NOT EXIST 1944_uimusic.wav GOTO :END
:1945_ERA
IF NOT EXIST 1936_uimusic.wav GOTO :1936_1945GL
IF NOT EXIST bob_uimusic.wav GOTO :BOB_1945GL
IF NOT EXIST 1943_uimusic.wav GOTO :1943_1945GL
IF NOT EXIST 1944_uimusic.wav GOTO :1944_1945GL
IF NOT EXIST 1945_uimusic.wav GOTO :END
:QUIT_MENU
GOTO :END
:BOB_1936GL
REN uimusic.wav bob_uimusic.wav
REN 1936_uimusic.wav uimusic.wav
GOTO END
:1943_1936GL
REN uimusic.wav 1943_uimusic.wav
REN 1936_uimusic.wav uimusic.wav
GOTO END
:1944_1936GL
REN uimusic.wav 1944_uimusic.wav
REN 1936_uimusic.wav uimusic.wav
GOTO END
:1945_1936GL
REN uimusic.wav 1945_uimusic.wav
REN 1936_uimusic.wav uimusic.wav
GOTO END
:1936_BOBGL
REN uimusic.wav 1936_uimusic.wav
REN bob_uimusic.wav uimusic.wav
GOTO END
:1943_BOBGL
REN uimusic.wav 1943_uimusic.wav
REN bob_uimusic.wav uimusic.wav
GOTO END
:1944_BOBGL
REN uimusic.wav 1944_uimusic.wav
REN bob_uimusic.wav uimusic.wav
GOTO END
:1945_BOBGL
REN uimusic.wav 1945_uimusic.wav
REN bob_uimusic.wav uimusic.wav
GOTO END
:1936_1943GL
REN uimusic.wav 1936_uimusic.wav
REN 1943_uimusic.wav uimusic.wav
GOTO END
:BOB_1943GL
REN uimusic.wav bob_uimusic.wav
REN 1943_uimusic.wav uimusic.wav
GOTO END
:1944_1943GL
REN uimusic.wav 1944_uimusic.wav
REN 1943_uimusic.wav uimusic.wav
GOTO END
:1945_1943GL
REN uimusic.wav 1945_uimusic.wav
REN 1943_uimusic.wav uimusic.wav
GOTO END
:1936_1944GL
REN uimusic.wav 1936_uimusic.wav
REN 1944_uimusic.wav uimusic.wav
GOTO END
:BOB_1944GL
REN uimusic.wav bob_uimusic.wav
REN 1944_uimusic.wav uimusic.wav
GOTO END
:1943_1944GL
REN uimusic.wav 1943_uimusic.wav
REN 1944_uimusic.wav uimusic.wav
GOTO END
:1945_1944GL
REN uimusic.wav 1945_uimusic.wav
REN 1944_uimusic.wav uimusic.wav
GOTO END
:1936_1945GL
REN uimusic.wav 1936_uimusic.wav
REN 1945_uimusic.wav uimusic.wav
GOTO END
:BOB_1945GL
REN uimusic.wav bob_uimusic.wav
REN 1945_uimusic.wav uimusic.wav
GOTO END
:1943_1945GL
REN uimusic.wav 1943_uimusic.wav
REN 1945_uimusic.wav uimusic.wav
GOTO END
:1944_1945GL
REN uimusic.wav 1944_uimusic.wav
REN 1945_uimusic.wav uimusic.wav
:END
CD "C:\CFS3 ETO ExpansionC"
ETOGLSwapper.bat
@ECHO OFF
CLS
ECHO.
ECHO.
ECHO WELCOME TO THE CFS3 ETO EXPANSION GLOBAL LAYER SWAPPER
ECHO.
ECHO THE CFS3 ETO GLOBAL LAYER SWAPPER WILL NOW CHANGE OUT THE GLOBAL LAYER FILES
ECHO.
PAUSE
ECHO.
RESENT
IF NOT EXIST "C:\CFS3 ETO ExpansionC\1945_qclocations.xml" GOTO :1945_ERA
IF NOT EXIST "C:\CFS3 ETO ExpansionC\1944_qclocations.xml" GOTO :1944_ERA
IF NOT EXIST "C:\CFS3 ETO ExpansionC\1943_qclocations.xml" GOTO :1943_ERA
IF NOT EXIST "C:\CFS3 ETO ExpansionC\bob_qclocations.xml" GOTO :BOB_ERA
IF NOT EXIST "C:\CFS3 ETO ExpansionC\1936_qclocations.xml" GOTO :1936_ERA
:1936_ERA
IF NOT EXIST bob_global_layer.csv GOTO :BOB_1936GL
IF NOT EXIST 1943_global_layer.csv GOTO :1943_1936GL
IF NOT EXIST 1944_global_layer.csv GOTO :1944_1936GL
IF NOT EXIST 1945_global_layer.csv GOTO :1945_1936GL
IF NOT EXIST 1936_global_layer.csv GOTO :END
:BOB_ERA
IF NOT EXIST 1936_global_layer.csv GOTO :1936_BOBGL
IF NOT EXIST 1943_global_layer.csv GOTO :1943_BOBGL
IF NOT EXIST 1944_global_layer.csv GOTO :1944_BOBGL
IF NOT EXIST 1945_global_layer.csv GOTO :1945_BOBGL
IF NOT EXIST bob_global_layer.csv GOTO :END
:1943_ERA
IF NOT EXIST 1936_global_layer.csv GOTO :1936_1943GL
IF NOT EXIST bob_global_layer.csv GOTO :BOB_1943GL
IF NOT EXIST 1944_global_layer.csv GOTO :1944_1943GL
IF NOT EXIST 1945_global_layer.csv GOTO :1945_1943GL
IF NOT EXIST 1943_global_layer.csv GOTO :END
:1944_ERA
IF NOT EXIST 1936_global_layer.csv GOTO :1936_1944GL
IF NOT EXIST bob_global_layer.csv GOTO :BOB_1944GL
IF NOT EXIST 1943_global_layer.csv GOTO :1943_1944GL
IF NOT EXIST 1945_global_layer.csv GOTO :1945_1944GL
IF NOT EXIST 1944_global_layer.csv GOTO :END
:1945_ERA
IF NOT EXIST 1936_global_layer.csv GOTO :1936_1945GL
IF NOT EXIST bob_global_layer.csv GOTO :BOB_1945GL
IF NOT EXIST 1943_global_layer.csv GOTO :1943_1945GL
IF NOT EXIST 1944_global_layer.csv GOTO :1944_1945GL
IF NOT EXIST 1945_global_layer.csv GOTO :END
:QUIT_MENU
GOTO :END
:BOB_1936GL
REN global_layer.csv bob_global_layer.csv
REN 1936_global_layer.csv global_layer.csv
REN gsl.lib bob_gsl.lib
REN 1936_gsl.lib gsl.lib
GOTO END
:1943_1936GL
REN global_layer.csv 1943_global_layer.csv
REN 1936_global_layer.csv global_layer.csv
REN gsl.lib 1943_gsl.lib
REN 1936_gsl.lib gsl.lib
GOTO END
:1944_1936GL
REN global_layer.csv 1944_global_layer.csv
REN 1936_global_layer.csv global_layer.csv
REN gsl.lib 1944_gsl.lib
REN 1936_gsl.lib gsl.lib
GOTO END
:1945_1936GL
REN global_layer.csv 1945_global_layer.csv
REN 1936_global_layer.csv global_layer.csv
REN gsl.lib 1945_gsl.lib
REN 1936_gsl.lib gsl.lib
GOTO END
:1936_BOBGL
REN global_layer.csv 1936_global_layer.csv
REN bob_global_layer.csv global_layer.csv
REN gsl.lib 1936_gsl.lib
REN bob_gsl.lib gsl.lib
GOTO END
:1943_BOBGL
REN global_layer.csv 1943_global_layer.csv
REN bob_global_layer.csv global_layer.csv
REN gsl.lib 1943_gsl.lib
REN bob_gsl.lib gsl.lib
GOTO END
:1944_BOBGL
REN global_layer.csv 1944_global_layer.csv
REN bob_global_layer.csv global_layer.csv
REN gsl.lib 1944_gsl.lib
REN bob_gsl.lib gsl.lib
GOTO END
:1945_BOBGL
REN global_layer.csv 1945_global_layer.csv
REN bob_global_layer.csv global_layer.csv
REN gsl.lib 1945_gsl.lib
REN bob_gsl.lib gsl.lib
GOTO END
:1936_1943GL
REN global_layer.csv 1936_global_layer.csv
REN 1943_global_layer.csv global_layer.csv
REN gsl.lib 1936_gsl.lib
REN 1943_gsl.lib gsl.lib
GOTO END
:BOB_1943GL
REN global_layer.csv bob_global_layer.csv
REN 1943_global_layer.csv global_layer.csv
REN gsl.lib bob_gsl.lib
REN 1943_gsl.lib gsl.lib
GOTO END
:1944_1943GL
REN global_layer.csv 1944_global_layer.csv
REN 1943_global_layer.csv global_layer.csv
REN gsl.lib 1944_gsl.lib
REN 1943_gsl.lib gsl.lib
GOTO END
:1945_1943GL
REN global_layer.csv 1945_global_layer.csv
REN 1943_global_layer.csv global_layer.csv
REN gsl.lib 1945_gsl.lib
REN 1943_gsl.lib gsl.lib
GOTO END
:1936_1944GL
REN global_layer.csv 1936_global_layer.csv
REN 1944_global_layer.csv global_layer.csv
REN gsl.lib 1936_gsl.lib
REN 1944_gsl.lib gsl.lib
GOTO END
:BOB_1944GL
REN global_layer.csv bob_global_layer.csv
REN 1944_global_layer.csv global_layer.csv
REN gsl.lib bob_gsl.lib
REN 1944_gsl.lib gsl.lib
GOTO END
:1943_1944GL
REN global_layer.csv 1943_global_layer.csv
REN 1944_global_layer.csv global_layer.csv
REN gsl.lib 1943_gsl.lib
REN 1944_gsl.lib gsl.lib
GOTO END
:1945_1944GL
REN global_layer.csv 1945_global_layer.csv
REN 1944_global_layer.csv global_layer.csv
REN gsl.lib 1945_gsl.lib
REN 1944_gsl.lib gsl.lib
GOTO END
:1936_1945GL
REN global_layer.csv 1936_global_layer.csv
REN 1945_global_layer.csv global_layer.csv
REN gsl.lib 1936_gsl.lib
REN 1945_gsl.lib gsl.lib
GOTO END
:BOB_1945GL
REN global_layer.csv bob_global_layer.csv
REN 1945_global_layer.csv global_layer.csv
REN gsl.lib bob_gsl.lib
REN 1945_gsl.lib gsl.lib
GOTO END
:1943_1945GL
REN global_layer.csv 1943_global_layer.csv
REN 1945_global_layer.csv global_layer.csv
REN gsl.lib 1943_gsl.lib
REN 1945_gsl.lib gsl.lib
GOTO END
:1944_1945GL
REN global_layer.csv 1944_global_layer.csv
REN 1945_global_layer.csv global_layer.csv
REN gsl.lib 1944_gsl.lib
REN 1945_gsl.lib gsl.lib
:END
CD "C:\CFS3 ETO ExpansionC"