ok, I figured something, here's the sequence of missing files (1-based index) - 12th, 24th, 37th, 58th
I did like a dozen uploads (multipart rars, different number of files, same part size) and this sequence is always as above. There were no problems with connection, so I suspect F&U somehow loose authentication data.
Hope it'll help to narrow it down and fix.
upd: different part size - different sequences, in my case - 100mb - every 12-13, 2mb - every 15-16