While I appreciate the discussion this question has spurred, I stilllll haven't been offered any solution to the problem. Anyone have any ideas? We seem to be talking about everything except the actual issue.
Too many variables, and too many different points of view and problems being discussed in this thread. My suggestion is to simplify, and specifically isolate what is at fault. I too have an

TV plus Onkyo setup, I have updated to 2.4, and am having no trouble getting Dolby Digital sound out of Handbrake encodes or rented iTunes movies. So...
Step 1. Isolate the problem. Pull the HDMI cable out of the

TV and plug it into the HDMI out jack on your Blue Ray player. Put in a disc with Dolby Digital and see if the Onkyo auto-switches to Dolby Digital. If it does, the problem is your

TV (factory restore

TV, update back to 2.4, and test again). As an alternative, switch to a toslink cable hookup to see if

TV is passing DD (don't forget to adapt your Onkyo audio input settings if you try this option).
If you've hacked the

TV don't reapply the hacks until you first test the unhacked software to verify you do indeed get DD.
It you rule out

TV with this test, the problem is either the cable or the Onkyo.
Step 2. Eliminate a problem with the cable by testing a different HDMI cable. If switching cables yields DD in the Onkyo (Blue Ray to Onkyo), try the working cable between

TV and the Onkyo with a known DD sourced

TV video. If you don't have any such video, I suggest ripping one chapter of a DD DVD with Handbrake (using the

TV setting) and using that as your "for sure" DD test video. A one chapter rip will only take a short while to encode.
To this point, you should have ruled out

TV and a bad cable.
Step 3. With the problem isolated to the Onkyo, try unplugging it, waiting a good while, then plugging it back in. A little power fluctuation recently had my Onkyo exhibiting some odd behavior (in spite of battery-based surge suppression)- but not your particular problem. A unplug-wait-replug did the trick.
Step 4. If you are definitely getting DD auto-switching from the Blue Ray, connect the

TV to that same HDMI feed. In other words, pull the cable out of the Blue Ray, and put it into the

TV. Then, try a "for sure" DD video via

TV and see if Onkyo auto-switches to DD. If that works, the HDMI jack to which you've previously had your

TV connected may be having an issue (but I bet Step 3 would lick that problem).
Step 5. Dig out the Onkyo manual (a glorious read for one & all

) and carefully go through everything- even the helpful(???) smaller print tips in the margins- related to enabling HDMI, DD, etc, checking to make sure all related Onkyo settings are correct. It's not that hard for Onkyo settings to be accessed accidently, and then changed (even a cat or dog can do it- no joke). Especially check and re-check the audio setup in the menus vs. the specific jacks to which you got stuff connected; and check your HDMI setup vs. your digital input setups.
Based on your feedback, my gut guess leans to the Onkyo, and I'm betting it will be solved with Step #3 or #5. But either way, if you'll try the above steps, you should be able to narrow it down to one component (vs. 3).