You should not be having reboot problems with EPUB files. Also transferring EPUB files using the SONY software gives you no advantage whatsoever, so dont bother doing that.
The only reboot problem I've seen with EPUB files is when clicking on links in the file.
I would suggest you wait a couple of weeks for the EPUB support to mature a little more.
As for LRF files. In my experience several feeds based LRF files cause the reader to reboot, but when this happens typically trying them again works.
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