The symptoms you describe make it seem like the Real Systems Module isn't running at all. Try starting the Real Systems Module (make sure trackIR is running FIRST) and then after the module has loaded CFS3, start a flight in one of the new Spitfires. Once you are in the mission, pause and minimize CFS3. Press CTRL+ALT+DELETE and bring up the task manager. Click on the Processes tab, and look for the following processes to appear in the list:
CFS3 Real Systems Module.exe
SpitMkII_Context.exe
SpitMkII_control_T0.exe
SpitMkII_control_P0.exe
SpitMkII_control_A0.exe
SpitMkII_control_R0.exe
SpitMkII_control_E0.exe
SpitMkII_Engine
SpitMkII_ETrim.exe
SpitMkII_GBreath.exe
SpitMkII_Gunsight.exe
SpitMkIIB_main.exe (this one depends on which variant you selected, might be SpitMkIIA_main.exe or SpitMkIIB_late_main.exe, etc)
SpitMkII_main2.exe
SpitMkII_RTrim.exe
Systems_Main.exe
Systems_TIR.exe
There could be some other similar named processes up too, depending on what is going on at the time. Let me know if any of these aren't showing up and it will help me figure out what the issue is.