I inadvertantly discovered a potential solution to a problem I know another user was having.
PROBLEM: When you click a thumbnail to open to the imagevue slideshow, the slideshow appears ON TOP rather than INSTEAD of the normal imagevue array.
SOLUTION: This appears to be related to the SIZE of your background.swf file. If you create a custom background that is fairly small (i.e. 1600x20px) this problem will occur. So create a larger (not sure how large, for me 1400x1050px) background.swf and this should fix your problem.
SOLUTION UPDATE: The 'transparency' of your created background also effects this issue. So if you're using transparent layers this may cause problems. I got around this by creating my transparencies in photoshop then importing (without transparencies) into flash.
I didn't go too far into this, but hopefully this will help anyone else having the same issue.
Christopher