I assume this is a modern monitor in that it already has an OSD. These store the display settings for each resolution in NVRAM inside the monitor. Two things are important here: the storage is limited, it can only save settings for a small number of resolutions. Second, the NVRAM is battery backed-up. Once the battery is flat, it won't remember any settings anymore and you have to readjust them each time. So I guess the latter is the case here.

Note, however, that this is generally speaking. I have no experience with the NEC MultiSync XV15.

Hey derSammier! Thanks for your response and input!

No OSD - there are knobs at the bottom for all adjustments (horizontal, vertical etc.). Just strange that not changing resolution only refresh rate would cause this.

I did notice that pin 9 was missing from the VGA cable of the monitor but I don't think that is what is causing the issue (it was common for older monitors to have that pin missing).

If there is no OSD but only knobs, the display has no way to remember settings for different modes. There is only one setting for all. And whenever you change something that uses a different frequency (resolution, refresh rate, whatever), the picture will be off. That's just how these old monitors work. They are completely analog. You can try to adjust it in a way that works for all the different modes you use by making compromises (e.g. accepting that the screen is not centered or smaller, but also not cut-off in other modes).

Ideally for your case, you set the desktop and the Voodoo to use exactly the same resolution and refresh rate.