Once you've run the AVGA resolutions tool, it should create a custom config file for every game with the proper resolution. What I'd recommend you try is to delete the mame32.ini file in your ini folder and then run it again with the "default" MAME32 settings, making sure you turn off hardware stretch if it is enabled.
Here's the recommended settings for MAME32 from the Ultimarc.com site (
http://www.ultimarc.com/avgainst.html):
Ensure the default settings in MAME32 are as follows:
Display Tab:
Run in a Window: OFF
Advanced Tab:
Stretch Using Hardware = OFF (if this is greyed out you have not switched Windows to 16 or 32-bit colour mode)
Scanlines = OFF
Resolution, Size = Auto (or select from drop-down list in game as required)
Switch Resolutions to fit = ON
Use DirectDraw = ON
You might want to try MAME (if you're intimidated by MAME, just get Emuloader -- it gives you a "MAME32-like" interface for working with the command-line MAME or MAMEPP. It's not too hard to setup, and it's just like MAME32 once you've got it running, except it uses MAME instead!)
The AVGA should auto-switch to the proper resolution for each game once the games are configured (using the AVGA "AVRES" resolution tool).
Hope this helps!
Kevin