I haven’t had time to troubleshoot it or get more information, but it appears that the strange errors I was experiencing yesterday after jumping between Crux and Arch were not, as I thought, the fault of retaining the home directory. A wiped drive followed by a standard installation also yielded the same errors on reboot, which had to be overridden by changing the “pass” digit in /etc/fstab.
I don’t have much time over the next few days, but I’ll try to make some headway in resolving what exactly ate half of my music collection and a few DVD rips. But for the moment I will amend my previous post and suggest that perhaps, this time, the fault lies somewhere between Arch Linux, my hardware and bad luck. :(