Update: Well, this program seems to be very hardware (video card, at least) dependent. On my PIII using a Gforce3 Ti200, I got regular native resolutions. However, on my new 2.8 P4 with an Nvidia 6200 unlocked to a 6700, I got the following very curious results (note, both computers are using XP SP2) :
First off, my Billabs multi-sync has various resolutions that many game resolutions fall under and the OSD displays them (ie: 640x224 for 240x256, 336x240, etc). In all games using soft-15 with the 6200, in the OSD I get 'user mode', with the timings at the bottom, and it turns out there are groups of games that fall under these, too. However, they're not all related by game resolution as is the case for the regular modes: for example, most 224x288 games are in the same group - except Jr Pac-man.
This is where it gets interesting. I noticed that in most games, the horizontal frequency shown in the OSD was 31khz - and often the vertical frequency being over 100! Even more interesting: I had my Monivision monitor hooked up to the other output, and expected it to turn off when loading games at native res. Not so. If got the same kind of image as with the Billabs - and the exact same in a few cases, no geometry difference between the two - and scan lines just as with the AVGA. Hmmmm.
What is happening here? To note, there are other differences, of which I've expressed before: the AVGA does some kind of strange brightness thing at low and medium resolutions (and my monitor makes a whine) that I can't replicate in Mame with stretch, and isn't happening with soft-15, though soft-15 does seem to make it a little brighter. Although, while I find the brightness of the AVGA games entrancing, those in soft-15 are easier on the eyes, particularly the scan lines.
There are also some oddities: regardless of either card used, there are games that don't sync - the Billabs will make a syncing noise, or both monitors will be blank and Mame32 closes back to the GUI - though they're not the same between cards. I haven't tried regular mame in a little while but recall observing the same behavior.
I also re-emphasize that windows at 1024x768 gives a scrolling desktop on either computer.