This seems to be an upgrade problem. I also have this problem with 13.10, but on a fresh 14.04 install the qjackctl systray icon works as expected. I am using the same version of qjackcontrol as the buggy machine though it is 32bit not 64.
This seems to be an upgrade problem. I also have this problem with 13.10, but on a fresh 14.04 install the qjackctl systray icon works as expected. I am using the same version of qjackcontrol as the buggy machine though it is 32bit not 64.