I had the exact same issue, along with other Yosemite issues which were what got me into Monkey in the first place, and got things working on my Mac by doing the following:
Uninstall drivers using the Line 6 uninstaller located here:
Applications/Line 6/Drivers/Driver uninstaller
(If you encounter issues, there is a detailed Mac OS X Uninstallation Guide here: http://line6.com/support/page/kb/_/computer-based-recording/computer-audio-set-up-and-troubleshooting/how-to-uninstall-line-6-drivers-from-mac-osx-r85 )
Then go to your folder Applications/Line 6 and uninstall your old version of Monkey by simply dragging it to the trash. Also remove POD Farm, Gearbox, whatever you are using with your interface. You will need it completely uninstalled to allow your Yosemite friendly versions to work.
Next, go to http://line6.com/software/?submit=Show&name=Line+6+Monkey to get a fresh download of Monkey with Yosemite support.
Once Monkey is newly installed, use it to download your new Yosemite friendly drivers and software.
This worked for me. I hope it helps!
