Hackrylix,
I've possibly run into some similar issues working with reaver on the command line and can share my experiences. If you're still having issues, maybe what I've learned will help. If not, then disregard.
I noticed I had to take down the 'phantom' monitor interface first (mon.wlan0), then wlan0, THEN start wlan0, and FINALLY put it into monitor mode to properly get it to work, and also NOT be stuck on channel 11 as others have run into.
So I had to:
ifconfig mon.wlan0 down
ifconfig wlan0 down
ifconfig wlan0 up
airmon-ng start wlan0
After all this, I had a virtual interface, mon0, that worked nicely for reaver.
Once side effect seemed to be that, in order to get back to being able to run Karma I had to reboot to get the 'phantom' interface back, but I'm sure those better than I could figure out how to revert without rebooting.
Hope this helps, but either way thanks for diving in and putting together a nice reaver interface. Much needed, and looking forward to it.