I have the same issue and I have Windows XP. I just manually change the global layer files and mission folder files.
Go into the global_layer folder and change the current files to their era names; for instance global_layer.csv to 1944_global_layer.csv and gsl.lib to 1944_gsl.lib.
Then change the era files you want to global_layer.csv and gsl.lib.
In the main CFS3 folder change the missions folder the same way; for instance missions to 1944_missions and 1943_missions to missions.
Not as convenient as using the swapper, but it only takes a few seconds.
There are also era-specific uires folders but I have never changed those.
I went to try gosd's method above, but my MASTERETOSTARTUP.bat and ETOGLSwapper.bat are already set on Read-only.