I have windows set to notify me of updates, but not auto-magically install them. Then I can install them at MY convenience. It just might work for you too.
Ahhh, my bad. Probably why the Tracker guide I found initially suggested not checking for updates, although that was for an older version.
Seems like a time-out on the update prompt could be a pretty simple fix. Or maybe just a non fold stopping info box that an update was available, and then go do it manually.
I don't think a change is necessary in this case. If you have the Tracker set to start folding automatically then you should either disable the automatic updater entirely or select the option to install updates automatically. (which will allow folding to resume after the update is installed with no prompts)