The SNES version seems to have better sound, but I think it's actually slower to run. Anyone know?

Some major differences:
Genesis has knockback, SNES doesn't.

Bosses are different:
In genesis, the Snorch has 3 tires which can hit him, but SNES only has 1.
Genesis Mailroom boss has a mini-level before it, which the SNES version entirely skips.
Genesis Zimbo is a boss, but in SNES he's just an obstacle.
SNES has about 5-6 seconds of loading between levels, which Genesis doesn't seem to have.

Additionally, it seems that the Key required to leave the level is sometimes in different locations, and sometimes there are different traps in sections...

I think this in total adds up to... Genesis is faster. It seems like the movement speed is significantly higher than SNES, to the point where someone playing SNES perfectly and someone playing Genesis with mistakes, will come out to the same time.

I believe you're right. I had considered splitting the leaderboards into two categories for the different versions. I don't know how well that would go over though.

just a tad late to the convo but yeah there does need a split in boards. i was watching the snes one and there are big differences compared to the genesis version, also nightmare difficulty mode needs to go up as a category too