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Upgrading from qjackctl 0.3.2 to 0.3.3 is not only painless but also recommended. Go ahead.

However, I don't really know whether it will solve your problems. I am far from comfortable in arguing about Ubuntu, as I it is not my distro of choice nor I have extensive experience with it. It is my knowing that all debian based package management is terribly picky about dependencies, but that's for a really good cause anyway. If it says that it will uninstall some particular package you better believe there's a good reason for it doing so.

It's just MHO.

Cheers