You will constantly get messages that tell you there is a recording conflict when there actually is no conflict. They will pop up while you are watching something and force you to pick one of two options, even though neither is correct. The PVR will occasionally slow to a crawl, lock up and reboot itself. The NAS box sometimes just stops working, and if you are not watching TV right when it happens, you won't see the message telling you so. You will only find out when you notice you have lost a weeks worth of recordings. Sometimes the system will just record black screens for you. That's neat.
Going through the list of recordings is a real pain. It will constantly revert back to the ordering method it likes, instead of what you pick. And it will do this every time you delete something within a folder. So you have to constantly fix it to find what you want. Another annoying thing is you cannot check scheduled recordings for the other PVR's in your system. You have to go to each TV to check!
Those are the main things off the top of my head. But there are lots more random bugs and glitches that only happen occasionally, but add up to be a real pain.
Once my contract is up, I will definitely be ditching the whole home PVR, and probably TV from Cogeco all together.