Where did you learn this? I can't find any info on which release it is.
The PC-DOS release of EWJ2 had pretty much all the graphics completely "remastered", this unfortunately meaning that they just don't gel as well in some places as the originals. Kinda like, say, the generally-liked classical graphics of Super Mario Bros., versus the remade graphics in Mario All-Stars. The new graphics are smoother, yes, but something about them just seems off at times. I recall the music being pretty rad, though.
If you were talking about EWJ1, I'm pretty sure it's basically the Genesis version (Intestinal Distress included but not Big Bruty, nor the extra level segments in the Special Edition), but with the CD music featured in the Special Edition. I think. Maybe. Not as sure about this one.