There really aren't any (that we know of) that cause issues with JFBConnect. JFBConnect itself has only one URL, and that's for the Login/Register page you get when you first hit the "Login With Facebook" button. Other URLs (for the Like button, comment box, etc) are all generated outside of JFBConnect.
Frankly, we've debugged issues with all the 'big' SEF extensions: sh404SEF, AceSEF, ArtioSEF, and probably some others. If you run into issues, our first suggestion is to always set the extension to 'skip' SEF URLs for JFBConnect. Beyond that, if you run into others, we should be able to help you work them out.
We use sh404SEF on this site. It's ok. Not the speediest, but gets the job done. We chose it because: it's the most popular, it's not encrypted, and it's pretty well supported (nowadays). The others area all tradeoffs in these areas, but you may find one that you prefer more.
Hope that helps,
Alex
Which SEO module best suitable with JFBConnect
