From DHS:

Earx wrote:
on the falcon the double vbl bug is caused by insufficient termination on the vga interface. hence, the vbl signal bounces back from the monitor to the falcon's hardware.

some vga monitors or adapters have higher resistance so the bug doesn't occur (probably as with the atari engineer's monitor).

the same thing could be affecting your mega ste. that's the only thing i can come up with.