I've just run into an unusual snap circumstance, in Inkscape 0.48.1 on Win7, 64-bit. You may well have it fixed by now. But just to be sure, I'll explain; and I can make a sample file if needed.
I have both a rectangular grid and axonomic grid in one file. For the moment, I unchecked "Visible" option in Doc Props for the rect grid. And I have "Snap to visible grid lines only" checked for both grids. What I first noticed was snapping behavior labelled "Cusp node to grid intersection" at places where there was no intersection of the axon grid. When I make the rect grid visible, I can see that it's snapped to the intersection of the not visible rect grid and visible axon grid.
It seems to me that snapping to a grid that's not visible is inappropriate (especially with 'visible only' engaged). Sometimes things that seem inappropriate to me, actually happen on purpose, for some reason I didn't consider though. Anyway, I didn't see anything about this at Lauchpad, although I don't always know the proper search terms.
Out of curiosity, I'll switch visibilities, to see if it works the other way around.... Ok yes, it does the same thing. And of course, with both grids visible, it still also snaps.
Actually, aside from snapping to a not visible grid, I'm not sure if snapping to the intersection of 2 different grids is all that appropriate. Although I don't know, maybe someone doing some fancy math could use 2 kinds of grids at the same time. So maybe having it just as an option, so it can be turned off if not needed.
Anyway, just for your info, in case it's news to you. If not, no worries, and thanks again for you great work on Inkscape

All best
