zoomkat:
I guess the question now is which temp files are associated with the arduino. There seem to be more than one type. Time to make a batch file to DEL jna*.tmp and similar.
On Windows, as long as you don't have any applications open, you can delete all of them. Those that are still open in a process will cause an access error and you can just skip that file. When I empty my temp folder, only 2 files remain, and both of them are tied to windows processes.