This has happened twice now; once on a vanilla Ubuntu 12.04 upgraded to studio and once on Ubuntu Studio 12.04 (which was installed over said vanilla Ubuntu install).
I get audio routed from a USB interface (Berhinger Guitar Link) through JACK (using qjackctl) and back out of the computer. Then I go back and adjust jack settings to improve latency and at a certain point, this same connection (hw:1 input, default output: system in to system out) stops outputting, while another program (hydrogen) still outputs. I'm not getting any xruns, either. This problem does not resolve after restoring default qjackctl latency settings. It also does not resolve after a reboot (It does, however, resolve after a reinstall ).
I'm running a Dell Optiplex 755. Core 2 Duo 2.54 ghz.