Running both windows-x64_4_3_1 as well as the4.3.1.jar I have the same issues on Windows 10.
Have reinstalled the .exe with no change to problem.

1. Rename PDF's not functioning at all
   • have tried with and without the "Upgrade external PDF/PS links to use the 'file' field
   • the library and the pdfs are in the same directory
2. Behaviour of "Cleanup entries" unpredictable, ranging from destructive to passive
   • sometimes the file links are erased when cleanup run on multiple entries
   • these can be recovered by selecting individual entries and running cleanup again
   • file links are incorrect. File type set to PDF:PDF and subsequent request to change file type fails as GUI buttons unresponsive
   • bibtex entry for file looks like file = {\:1-s2.0-S1364815212001879-main.pdf\:PDF:\:1-s2.0-S1364815212001879-main.pdf\:PDF:},

Running development version doesn't clean up the bad file paths but running Cleanup on individual entries does change the pdf name to the specified pattern and appends that to the path. Manually emptying the file path for each entry seems to be the only way around that particualr problem

JabRef version on

• I have tested the latest development version from http://builds.jabref.org/master/ and the problem persists

Steps to reproduce the behavior:

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