I don't know if this is the software bug or intended functionality, but
when the "Mute Mains for Mic Record" (POD Farm->Preferences->Hardware) option is activated, listening monitors are muted - not just for the Mics (sensible feedback protection) but for instruments/line inputs also (for what?).
I think the instruments/line inputs should not be muted.
tested on:
OS: Windows 7 SP1 x64
audio: UX2 (driver: 4.2.7.7, USB firmware: 1.02, POD Farm: 2.59)
hardware: Xeon W3690, 48GB RAM