Well there is 2 issues,
1. Explorer.exe intrudes on the colour palette for 25 colour ddraw games. as long as you use more then this its fine.
2. For those games that use a 256 colour palette, there is a strange freeze issue that occurs in both video and input, theres no direct reason as to why, expect that using applications which draw an overlay (Fraps, Skype, Winamp) to occur sooner.
I've not been able to reproduce the freeze very easily on games that use 16bpp, such as emulators, but on yours there is definitely an issue with texture scaling.
Btw, i really would like to see Kega filter support in a future version of jnes. or maybe a HQ4xS filter