Fixed up the problems with ibmtr, a swift ioremap here and an ioremap there and everything is working ok.
Now I've got access to my test machines I am going to beat the hell out of the driver this weekend before I release it again.

Found out why ssh has died, turns out the debian package upgrade put back the file /etc/ssh/sshd_not_to_be_run, so, of course, after the reboot sshd didn't start up. I think I need to find the ssh package maintainer and slap them with a wet fish.

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