@DoctorOhh: my guess is calibre is hitting an out-of-memory problem, because the portable edition is 32 bit. This would be consistent with the cache file sizes you report if the error is happening while the cache is being written.
I need to rethink how to write the cache. The current system makes a copy of the cache then writes it to the disk. I probably need to find a way to write it book-by-book.
Any fixes for this will be in calibre, so unless you are running from source (and IIRC you are not), experiments will be tied to calibre releases.
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