If your using Photopost 5.5 there is literally no way that this issue could exist that I am seeing
This is the code in bulkupload.php
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With this code basically what it does is check to ensure the uploaded file is not the same name as a file already present and renames it. So literally if I am understanding what your saying you did I dont see how that could ever happen in 5.5
You can do a simple test to confirm what I am saying.
Upload the same file twice to different categories and you will see that when the second one uploads its name will be slightly different. You can then move it as you did before and see that the action works perfectly. Now in way older Photoposts it only use to check filenames in the same category and thats why I said if you had a way old Photopost that I could see something like this happening and we did fix that a ways back to check all filenames