Can you give some more information about your batchfile, how do you run two mame versions with one frontend?
I just wrote a simple script like this:
cd\mame
if "%1" == "dkong" cd\mame162
if "%1" == "kungfum" cd\mame167
mame64.exe %1 %2 %3 %4 %5
Then you just set the batch-file as the Mame executable in the frontend. Note that you'll need separate folders for each Mame version, as many of the supporting files aren't compatible between versions. Rom sets aren't necessarily compatible either, but I never had any problems with that in particular.
The newer versions of Mame are far better optimised though, so my initial reason for doing this doesn't exist any more. All m62.c games now run nicely, even with normal hardware.