Ok - have you been able to run the 3d desktop effects smoothly, then? If you have, that probably means you graphics drivers are fine (and that you're using proprietary graphics drivers that take advantage of hardware accelaration); if you haven't, you're probably still using some non-proprietary drivers, which are good (and often more trouble-free than proprietary ones as I've noticed personally) but don't simply (usually) provide hardware 3d accelaration. Unless you run 3d things like 3d desktop effects or games, you don't necessarily need proprietary drivers; if you do want such things, they're usually your only choice.
Running this in a terminal:
should provide some information about your graphics driver situation; there's a lot in it, but if you just want to see if your 3d accelaration is working, check the line that talks about direct rendering: enabled means your drivers seem to take advantage of your card, disabled means your driver might not support the fancy 3d stuff that your card could do.
If you're not using a proprietary driver (it's all in /etc/X11/xorg.conf, look for a Driver line in the graphics card section), you shouldn't have big problems. At least I haven't seen much odd things when using those, but if you on the other hand are using a proprietary driver (for example 3d desktop effects work fine), it might easily be there are some situations where it starts playing tricks on you. It depends on the exact problem, but sometimes you may have to resort into reinstalling the driver (using your package manager software; that's the easiest way of doing it, just select the nvidia driver package that is installed to be reinstalled). Sometimes just restarting X helps (CTRL+ALT+BACKSPACE), but if rebooting didn't help, that probably won't either.
Your graphical server (X) configuration is stored in /etc/X11/xorg.conf file, which should be editable by root only. You can see what's in there; in case you edit it, make a copy of the original file so if you run into trouble you can simply move/copy the backup copy over the "real" file and get your original settings back. For example you can see what the Driver line says about your graphics card: for nVidia cards it should be, if I'm right, "nv" for the non-proprietary (no-hardware-accelaration) driver and "nvidia" or something like that if you have installed the proprietary driver. You can try to switch it to "nv", save and restart your X and see if it helps, then change it back to "nvidia", save and restart X and see if it makes any difference.