Is it possible that you have shortcut keys enabled and turn the tracker on that way?
Let us know it happens even with the shortcuts disabled.
I mainly use the timetracker appliction on a Mac OS X computer. It is very easy to quit the application.
I take it you are using Windows PC? Is there no such option? To simply exit the application when you're not using it? (Then you would not need to worry about it switching when you don't want it to.)
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