I have a 52" XBR6, ps3, xbox, and comcast hd cable box all hooked up through onkyo hts6100 via hdmi.

I am experiencing bad juttering issues with scrolling on the bottom of the screen (watch a lot of ESPN so it's annoying). Any ideas on a fix?

Same issues with both standard and high motion flow.

Should I skip the reciever for the cable box and go straight to the tv then optical to reciever or is this a TV issue not an Onkyo issue?

I saw this problem when installing my in-laws' Vizio LCD. I was ready to write it off as a bad TV, but found that it was because both the cable box and TV were trying to re-size the picture to full screen. I set the cable box to pass-through the video, let the TV re-size the picture, and the problem was fixed.

In your case, you could have all three components vying to do some type of picture processing.