I've had this problem ...
'twas when gftp couldn't resolve a domain name .. and I left it running knowing that soon enough my net connection would come back up.
my root partition (100GB) went from 10% to 100% in 12 hours :shock:
when I tried to find out what was going on, I found nothing.
no big log files
no big .xsession-errors
nothing !
I logged off (not reboot) and watched as the disk emptied itself, until it reach 11% full ... whoch was expected.
the reason was the error were not being flushed to the log files ... they seem to be sitting nowhere, but using disk space ... go figure