I've seen this happen for a few years now, old (but super annoying!!!) bug.
My setup:
Laptop user, dual monitors at work, dual monitors at home. I put my laptop to sleep when I leave work, dock it at home and start it back up.
Bug description:
At first everything worked fine, fences stayed on the primary monitor in both cases (primary being the one with the Start bar). Periodically however (weeks, months), Fences loses track of which monitor is primary and puts all my fences on the opposite monitor. Windows is keeping it straight (start bar is OK), but Fences loses track. It will stay like that until the bug happens again (more weeks or months) and it will switch back.
I experienced this on XP, now still seeing it on Win7. I recently experienced this with Fences 1.01.143.