Well I spent some time with the 809 today, finally. About an hour updating firmware that said nothing about fixing my issue but it did, and some research and playing. Still a long way to go but what I know so far:
1. Latest firmware eliminated my double handshake issue when powering on the 809 from standby. Of course this was not a problem when I was not using image processing from the AVR.
2. Firmware did nothing for dimming of brightness in custom mode, same thing, but one could and should just adjust the brightness and contrast in there because that is what the custom mode appears to be for, If you want to use that mode and calibrate. See below.
3. Now I don't feel like going through a full calibration right now and that is pretty much what the manual says you have custom for and you ought to know what you are doing or have a ISF pro do it. But wait, I paid for this video processor and want to upscale to 1080P with it. Well I also paid for ISF settings so I selected ISF day and bingo. Great pic right there in my lighted man cave. Will try ISF night next time I fire up the PJ. There are other modes too.
4. Finally got off my lazy arse and just googled TV logic mode only to discover it is an old legacy Onkyo DSP mode. Then I found it in the manual under that section(dumba$$). So I figured out that when a crappy commercial comes on it happens every time, not all commercials. Dig into manual and see that it must be in the Listening Mode Preset. Went there and saw all were defaulted to last valid. Well not sure if it was 2 channel or Mono/multiplex so I just went in and set all sources to output Dolby EX or direct and that is working fine for now.
So not a bad day today along with all the other crap I had to do. Shortly it will be time to crank up the Godsmack concert DVD and give it some he!! Last night's audition was not impressive at all. Not sure what I have changed since the last time I fried one of my front speakers listening to that but yesterday that DTS soundtrack could muster nowhere near the volume. I am sure it is in the menu somewhere that I need to adjust something. Get that sorted out and I am going to be a happy camper. Hope this helps someone.