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73416ba
(Get the code!)
OK - that re-factoring (Single/unique application instance control adapted to Qt5/X11) was listed in the release notes to 0.4.1.
I am not sure that allowing more than one Qjackctl instance is a good idea. Some audio applications require JACK to be running, and other start it themselves. This may cause users to get in a real tangle. But I will leave that to my more experience Ubuntu Studio team members to confirm.
As a quick and temporary fix, I think the patch to build with QT4 would be the best. All of the above 3 issues are solved, and the QT4 libraries are required anyway for other often used audio applications (e.g. ffado).
I have created a new ticket upstream about the freeze with Dmitry's suggestions. Hopefully we will get a better fix from upstream for the next release.