Sure enough... I unchecked the checkbox, and left it that way for a few days, and during that time the Options window never popped up on its own. As an added test, I checked the box again, with the frequency set to 1 hour, and the Options window came up roughly an hour later.
On a related note, the update check frequency box allows the user to manually enter arbitrary values, but it seems these won't work unless they're integers. In other words, I tried entering "0.025" in the box, figuring that would give me an update interval of 0.025 hours (or 1.5 minutes). While I was able to enter and save the value w/o any errors, it didn't seem like the app was actually checking for updates that often - or maybe it was? But the Options window wasn't popping up...
Hope this helps!