This is almost exactly the issue with the reading time statistics. I believe I've posted about the problem in the past in the future kobo touch firmware thread and listed on a high level the problems you've described in detail here.
Opening the in-book menu via touching the center of the screen doesn't mess with the timer as far as I can tell. Using the options within will though. If you bring up the in-book menu to simple check the time and then close it it will not mess with the timer.
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