I have the Onkyo 605. Yes, it can decode TrueHD (plus DTS MA & DD+) - but ONLY from a High-def player that can send it the audio over HDMI 1.3 in compressed bitstream. Only the A35 HD DVD player can do that, and the Samsung 1400 & Panny 30 on the BD side.
But the A2 is perfectly capable of decoding DD, DTS, DD+ and TrueHD internally, and then send that out as PCM over HDMI to your Onkyo.
In the Setup Menu on the A2, in Audio, both the Optical & HDMI should be set to PCM (even if you're not using optical, to be on the safe side).
You say you have gone through all the settings on the A2. How about the Onkyo? Have you assigned the HDMI audio input (HDMI 1 or 2) to the correct Viewing source? (VCR/DVR, CBL/SAT, or Game/TV)
I had an XA1 audio & video playing perfectly through my 605, and now have an A35 doing so as well.