After my wipe and reinstall experiment, there are still a few little glitches (above and beyond the fact that I’m still running my RAID1 in degraded state because the disk it’s supposed to be mirroring to is being replaced). One of the most annoying was my hourly “rsync to the external hard drive” – my own home grown equivalent to “Time Machine”. About once a day it was freezing up, usually during the first big access to the drive, which is a “rm -rf” on the destination directory. And once it froze up, it really froze up – there would be dozens and sometimes hundreds of processes that wouldn’t end and couldn’t be killed, most the hdparm and smartctl commands that munin issues to detect the drive status and temperature. The only way to get those processes to end was the turn off the external USB cradle. This didn’t happen before, so I don’t know what’s going on. But I suspected that something is being more aggressive about spinning down idle external drives, so I issued the command “hdparm -S 0 /dev/sdd” and that seems to have solved the problem.
Other glitches – the dvd player application exits as soon as you start it. Also, I just had a notification in the system notifications area that there were upgrades to install, so I clicked it and it brought up the updater app, but when I clicked “Install all updates” it told me it couldn’t because I hadn’t authenticated. I’m pretty sure it’s supposed to prompt for your password and authenticate you first. So I installed them from the command line using aptitude. Nothing I can’t live with.