Unless the files were queued to the folder they were uploaded to, this seems highly unlikely, FlashFXP has (always) a routine which compares the current folder with the one defined by the queue if there's any difference FlashFXP will attempt to change dirs, check the path again, if the path is now correct it will proceed to transfer the files, if however it's still incorrect it will fail.
I did some basic testing and it appears to be working as designed.
If you are able to reproduce the problem can you please include a copy of the status text winow, also the path the file was intended to for and where it actually ended up.
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