I'm using 3.2.0 now, but first experienced it with the previous version (3.1.6?).
When uploading a file that already exists on the server, I choose the rename action and append '.new' to the filename. When I click OK, I'm once again prompted with Target File Exists even though no file with that name (the one with .new tacked on the end) exists on the server. I can choose the Overwrite action this time and the file is uploaded with the .new name so this is really just an inconvenience.
I haven't used the non-portableapp version of FileZilla so I can't say if this issue exists in that version or is specific to the portableapp version.
[Edited for transposed digits in minor version numbers]
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Issue exists in 3.2.1, also. But then since there was no response to the early post, I'm guessing this is the wrong place to bring this up?
Try a local install of FileZilla to be sure you can reproduce the issue with your same server. Once confirmed, report the bug to the FileZilla folks.
We make it portable but don't fix bugs within FileZilla itself.
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