If it came from Oppo, it should have the latest firmware. To check, here are the instructions from Oppo's support page (which lists the latest version):

• Press Setup on the remote controller
• Enter 9210 on the remote controller
• A menu will pop up to show the firmware version of the OPPO player.

I agree with the Outlaw tech in principle: the Oppo's on/off status should not affect the 990's IR sensor or ability to receive remote commands. The operative word there, however, is "should" - and strange things can happen sometimes. I think the list of things to check is a good one, and I would probably not include the DVI cable on your list (I have both a dual link and single link in my system - single link provided by Oppo between it and the 990 and a dual link from the 990 to the TV). Let us know what you find.