Audacity is really lame with Jack. It's [retty lame in general, actually, but unless something changed recently, the fact that it has no native Jack support is pretty bad...
well, audacity uses portaudio to talk with jack, which is not generally bad ... i guess it is more a problem, how audacity talks to portaudio, than portaudio's jack backend ... i am using portaudio myself to connect nova to jack and it is running really stable ...
cheers, tim