He's right. To run the NES Classics use VBA 1.80 Beta 1 or better, as even with the altered settings they will not work on 1.72, which is why there is slowdown. 1.80 fixes that.
Also if you search, there was a topic somewhere that provided an altered vba-over.ini file that you must use as well, just search for vba-over.ini
Mods: Sorry if this topic was considered dead, I just wanted to help confirm how the games run on VBA.
On a side note, Id rather play the games on an NES emu cause the graphics are not all that different and neither is the gameplay.