The problem was fixed (a little bit) by deleting the com.apple.audio.AggregateDevices.plist file from the root user account. I have done this on both my laptop and desktop setups. The laptop was kind of old and did not like editing in Premiere that much, but FCP was fine. I did have to transcode everything though.
The laptop has been replaced with a newer version and Premiere works great. I still deleted the com.apple.audio.AggregateDevices.plist file though just to be sure.
I hope this helps.