What are the glitches at the top of bottom of each hour you are talking about?
There's a roughly 1-second drop out at the top / bottom of the hour (really 29/59) on hopper and joey. This is true on live and also occurs at the original :29 and :59 when you are playing back a DVR event. In short, it's an actual issue with the datastream.
I have never noticed this on my Hopper and Joey despite widespread reporting of this bug here.
I've often wondered if it's related to PTAT, as I have that feature disabled on my system.