@ h0ffman - yes, is the short answer.
I've experienced differences with code running on the emulator versus the real thing several times.
First blitter line draw routine I did worked fine in the emulator, but glitched *one* and *only one* 3d object when run on the real thing. Very odd, never found out what the problem was - just recoded the line draw routine!
Also have (very) slight glitches on my Kefratraz bars routine when run on the real thing but they work totally fine in the emu.
The moral is just what you said - always test on the real thing before releasing anything cos you never know 100% if it'll work right or not.