|QJoyPad 3 Documentation: Distributed with QJoyPad 3.4; available online at http://qjoypad.sourceforge.net/doc/doc_index.html|
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QJoyPad doesn't work well when there are two or more instances open; for that reason, it uses a file to tell whether or not it's already running. Every version of QJoyPad has done this, but in version 3.4, where that file is kept was changed to make the program more compatible with certain distributions.
If you're seeing two versions of QJoyPad open at once, that means that either one of those is QJoyPad 3.4 and the other is an older version, or that you're running an older version of QJoyPad on a system where you don't have write access to /var/run. In either case, you should just make sure that you are running the newest version of QJoyPad and that there are no other versions installed on your system.
If you really want to keep earlier versions of QJoyPad, that's fine! Just remember that if you do, it's possible to have two instancesrunning at once and that that can cause problems.