I just recently updated my touch from 2.1.5 to 3.0.1, and it started randomly freezing. It would work for half an hour, then it would freeze. At one point I put it, frozen in my purse, because I didn't have a paperclip to reset it. It came "unfrozen" about half an hour later. I noticed when I pulled it out of my purse, and the page on the screen was different and the dictionary was hilighting a word. That's when I learned I could wait for it to unfreeze ... not that waiting half an hour to be able to turn the page is reasonable.
I played around with it a bit, and it wasn't due to the books, wasn't due to where I was tapping, and was a pretty regular occurance -- multiple times a day, which it sounds like yours is less frequent.
If you have the patience, I'd play around with it a bit more. See if it happens when the battery gets low, or only if you haven't turned it completely off recently, or only on larger ebooks or only on a particular file.
In my case, I contacted Kobo and they swapped it out for another reader. Still not sure if it was an update problem or hardware that's starting to go bad.
But, best of luck. I hope that you can solve the issue yourself, and if not, that you can get it sorted with Kobo. Like I said, the more troubleshooting of the issue you can do before you contact Customer Relations, the smoother it goes.