Crowbar is working OK for me in FW6. I’ve seen this error before though. It’s usually because you’ve put a crowbar inline at the end if a paragraph. Putting it in a paragraph of its own fixes the problem, and the ‘extra’ paragraph is removed.
I’d be a little wary of working on sites you started in FW5(.5) in FW6, at least until any .0 bugs have been ironed out. You should have a [FW5.5] backup of your file.