I am typing this out of my memory, as the affected box is in the studio, not here. But better a bad bug report than no one:-/
This is an install of ubuntu studio 10.04, with ardour 2.8.6, and jackd 0.118+svn, I presume (I used jack2 before on another install, but I don't remember hacking around in the ubuntu one to get jack2). Ardour quite often is disconnected from jack (for whatever reason, usually _not_ during recording) and the real bummer is that it fails to reconnect the channels/tracks to jack ports.
It can connect to jack, but the client name changes from ardour to ardour-01 ... ardour then tries to connect ports for the non-existent client "ardour". That doesn't work, of course. I have to exit ardour and start again to get the connections working. This is very reproducable once you got ardour disconnected by some other mischief (I'd need to try if this happens on user requested disconnect/reconnect, but I doubt it).
This is is also quite frightening since ardour promises only proper saving of projects when the jack connection is right ... and I had to reconnect things after recovering from the ardour-01 confusion. This gives us (ardour2/Linux and me) really bad press when we (the band) are in a recording session and my band waits where I have to fiddle around with that strange Linux thing:-/
Question is now: Who is to blame for the client name mismatch? Ist it ardour, is it jack? Should ardour verify which name it gets assigned and not try to connect ports for someone else (named "ardour" where ardour is named "ardour-01")? In any case, I hope this one is resolvable...