The pause/flicker is the time it takes for the display to change to the different resolution of the new channel compared to the prior resolution for the old channel. Different displays do this faster or slower, so it is something that is dependent on the display design.
I use the pass through and let the TV do all the scaling but it is faster with my Panasonic plasma than with my old display before it. If you let the cable box do the scaling by having everything get scaled to only one output resolution you are having a likely inferior cable box do the scaling and will have more artifacts from this. If you do not see these issues letting the STB do the scaling then go for it. I do notice so I will live with the very brief flicker while the display adjusts to the resolution when changing changes.
You can confirm it is the TV adjusting while in pass-through mode in the STB by switching between 2 channels that you KNOW are the same resolution.
Hope this helps!
__________________
Denon AVR-887
Klipsch RP-5 Pwred Towers (mains) (525 watts peak each 12"Subs)
All Klipsch RC-25(ctr),(2)SS1(surr),(2)SS1(rearSurr)
Toshiba (2)HD-A20,PS3,BD35
For SACD/DVD-A Samsung HD-841
Panny 50pz80u plasma SETTINGS
RCA HD50LPW162 50"DLP w/HD2+
SA 3250HD
47" LCD+Yamaha5790+HD-A1(bedroom)
Harmony 680 + (2) 670s (amazing remote/support)
Game room with Onkyo receiver & B&W Speakers
The_Cable_Game
Take the high ground and be happier 
|