I am having the same problem.. almost.
After a while of using it, 20min or so, it starts to kill my cpu. I noticed it earlier when a mp3 i was listening to started locking up. I checked and flashfxp was using 90+ cpu when I transfered files. I was only transfering a couple of files, CSS so they were small. If I close flashfxp and restart it everything is fine for another 20-30min or so.
Going to try uninstalling and reinstalling in a few to see if something happened from a windows update or something.
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I have no idea why my user name is my email lol. Can that be changed somewhere?
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