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If you sharing plugins between the 12 and 13 this can happen, ie if all your plugins are in:
Having them in one spot is easier for support though.
You can put them individually in:
Library/Application Support/Filemaker Pro Advanced/12.0/Extensions/
Library/Application Support/Filemaker Pro Advanced/13.0/Extensions/
But you will have two copies.
I wish I could remember which plugin caused me the issue.......
I'm finding that if I have the script that closes and exits the program, just close the files. The Exit manually, most of the time it exits with out a problem. Apparently having the exit FileMaker script step exit the program is causing an issue.
I think most of the plugins are in the .../12/Extensions or .../13/Extensions folder, but not all. Depends on when/how they were installed.