Actually, there's a checkbox within Fraps that says something like "Record Windows Overlay" (or anything probably totally not like this... >> ); it allows you to record anything you want at any time, be it your plain boring Windows background or the contents of your RGSS(2) Player.
This feature, however, I've noticed to be very different between releases (of Fraps), even without any notification in the changelog. Therefore, you might still not get the results you need, or need to do any post processing, so after all, you might be better off with another program.
EDIT: I've tried to look for it on screenshots, but haven't been able to locate it... I'm currently using Fraps 3.something at home, which I'm fairly sure not having this feature, which would mean it's in one of the 2.something versions...