Because it is very slow. Look at the benchmarks I made (on a different machine):
http://www.amiga.org/forums/showpost.php?p=746617&postcount=14
WOW! According to your benchmarks, E-UAE is massively ridiculously faster than FS-UAE.
Did you wait a while and then repeat the benchmarks?
Because either FS-UAE just plain sux, or your computer had launched some sort of high priority background task at that moment, like an update-checker or virus checker or your forgot you were rendering the new Lord of the Rings 4 in the background
