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i think your problem is not related to rtirq, not even remotely :/

as you must know already, rtirq is supposed to help you fine tuning irq service threads priorities (whatever that is). this is a kernel feature only existing on the preempt_rt patched ones or on latest 2.6.39+ when started with "threadirqs" boot line option.

again, it doesn't seem to relate to your primary issue--you're missing system wide privileges to run processes with realtime scheduling, which is paramount for jackd, i may say.

i suspect that, as a consequence of your distro upgrade, the kernel was also upgraded, and probably the old limits.conf hack is not enough anymore.

could it be, a cgroups issue?

hth.
cheers