This is a bug in libfreebob 1.0.0. Freewheeling was not tested when this version was released.
In our maintanance SVN branch for 1.0.x this problem is fixed. Once we have enough confirmation regarding whether the issue is resolved with this fix, we’ll release a 1.0.2 maintenance release for the binary packagers.
You have two options:
wait until the 1.0.2 version comes available as package for your distro
checkout and compile the 1.0.x maintenance branch and compile it yourself.
If option 2 is something you can do, I’d really appreciate it if you could give some feedback on whether it fixes the problem or not.
for the record of ardour forums, the latest 1.0.2 svn works like a charm.
ardour now exports cleanly and as a bonus stopping and restarting jack now it always successfull.