I do get a bit of delay between video coming up on the screen with when switching modes for other players of a few seconds. Other AVR I have owned and still own, was lot faster at responding with the video switching. I've gotten used to mine. You might have to get used to yours but yes its annoying.
I haven't seen any of he other issues with jog shuttle and when switching sides it all looks normal on my, Onkyo TH SR-875.
I guess setting your Onkyo, back to factory settings might not clear the issue?
Press buttons (Standby and VCR/DVR) at same time, restores back to factory settings with word CLEAR on the display screen.
Upscale is great on it makes Laserdisc worth watching more and more.