What I need to do is to shift the monitor's positioning of certain screenmodes. I know that it can be done as AdvanceMAME's monitor configuration used to be able to do it.
Advancemame can resize the image, but not without lines missing or added, which results in various kinds of artifacting. That's the nature of things. Perhaps when you used Advancemame you didn't know what to look for to know it wasn't perfectly displayed.
No, that's not it either - clearly I'm doing a crap job of explaining myself
It's not artefacts or resizing, but the positioning of the viewable area of the screen. AdvanceMAME's tool (advv, from memory) to set the screen up allowed the viewable area to be shifted in a manner similar to what MAME does (as you suggested), but it allowed me to do all screenmodes to a larger degree that meant that I could have (for instance) a 224x240 @ 15KHz and an 800x600 @ 31KHz in exactly the same spot on the monitor.
The NVidia driver tools allow shifting of the 31KHz screenmode's position to a certain degree, but not far enough to avoid adjusting the horizontal positioning on the monitor without mucking up the 15KHz screenmodes (remember that my monitor can do all of the 15KHz modes natively and completely accurately).
The reason why I've been trying to get the various screenmodes all lined up is so that I could have a non-interlaced screenmode for MaLa. I've settled for a 640x480 @ 15KHz with flicker that isn't too bad because of the background image, which means that everything is positioned exactly correctly. Once I add the tinted glass over the screen, I'm imagining that the flicker will be even less of an issue.
To be honest, I think part of the issue is that the monitor is so old that it doesn't save settings (no OSD) - if it could, I wouldn't have an issue. When I was using AdvanceMAME, I was running DOS with a TNT2 M64 card, so all of these factors combined may well mean that this is why the issue never came up then.
As it is, the games look pretty much as good as they can probably get with MAME (correct refresh rates, fullscreen, scanlines from the monitor (not emulated) and no tearing), so having a slightly flickering front end is not worth losing too much sleep over