The fix would probably depend on how the code you have is written. Perhaps it would be easier to help if you posted the source of the script either in full, or just the relevant bits (if you know which parts may be relevant).
Oh, and regarding the errors, I personally am not experienced enough with ImageMagick/PerlMagick to understand them at this point. Seems like they have something to do with layers, but that's just an uneducated guess. Again, it'd probably be easier to help if the source was available here.
-- Sid