No, haven't heard of that issue at all. We know of quite a few sites that use JoomFish with JFBConnect, including some that have already upgraded to JFBC v4.0
I honestly haven't played with JoomFish too much, but if there's a way to tell it to 'skip' URLs for JFBConnect, we'd definitely recommend doing that. Some extensions that mess with our URLs cause problems with our communication between your site and Facebook. Also, if you're using an SEF extension (not Joomla's built-in SEF), you should set that to skip JFBConnect as well for the same reason.
If you send us the URL for your site, we can take a look and let you know what we see. From what you describe, it's likely something we can diagnose from looking at the front-end HTML on your site.
Thanks,
Alex