Why don't you try out the sneaky peek release here:
http://www.omnigroup.com/products/om...oad/sneakypeek
There is some mention of improving behavior with Spaces in the release notes; if you're still having the problem with that version, I'm sure they'd like to hear about it sooner rather than later. You don't have to continue to run the sneaky peek if you're not comfortable with the idea, just figure out if they've got a fix for your problem yet.