You shouldn't have to use bat files really...but it usually does work. However, the preferred method is using shortcuts...
Try adding {safelaunch} to your emulator_commandline, ie:
emulator_commandline pc{safelaunch}
I looked through the code and this should work, although I noticed a slight mistake which might prevent it from making any difference. If it doesn't work, let me know and I will compile a fixed version...