Alright, this is strange...
I was running at an average of about 46 MIPS. Then I installed MegallanII and it dropped down to about 34 MIPS. I've never heard of software reducing MIPS before, but what ever...
So I deleted my OS folder and re-populated it with my back up of a clean OS 3.9 install with both official Boing Bags. Oddly enough, my MIPS remain at 34 instead of 46, and I know I didn't change FS-UAE's settings anymore so what could cause something like that to happen? And why isn't it getting closer to 100 MIPS anyhow? My 1200 with 80Mhz Apollo is faster than this.