Are your No$gba and ROMs both in My Documents folders? At least make sure your BATTERY subfolder is not read-only.
Ensure you are using No$Zoomer v2.3.0.2.
Also make sure you are using No$gba v2.6a. You can check the version under Help -> About.
Obtain and put biosarm7.rom, biosarm9.rom and Firmware.bin into the same folder as No$gba and No$Zoomer (google if you can't find them, or just dump them from your own DS).
Those are all the standard solutions. Try them, even if they don't fix *this* problem they will help to make things better for you. If the problem persists, though, do continue to tell us about it.
Edit: That's assuming that your computer is not powerful enough to play DeSmuME at decent speeds. If you can use desmume then just
use it, it should solve your problem for you without much fuss.