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Thought I'd post the resolution...
It turned out to be a corrupted file system. Calling e2fsck from single used mode fixed it. I spotted that when the system seemed out of space, a kernel error messge from the file system module reported that there was an ambiguity in something called a block group.
I didn't think of running e2fsck because it was run when the machine rebotted. Obviously it get run in such a way that not all errors get fixed.
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