That doesn't sound like a firmware problem, or rather, a problem that 3.09j might address where a reinstall of 3.09 did not do the trick.
A few things to check:
1) Clear all the "temporary" speaker volume trim adjustments -- the ones changed using the buttons on the remote. To clear all of those in one go do this:
-- Save User Settings
-- Reload Factory Defaults. (If you lose video at this point, continue via the Front Panel display.)
-- Reload Saved User Settings. Since the "temporary" settings are not saved, this resets all of them for all audio formats.
2) Go into each Setup > Source Setup and make sure you have Dolby Volume set to OFF for every Source line.
3) Press the Dynamics button twice and make sure you don't have dynamic range limiting turned on. See Section 4.8.10 of the Manual. (This is not likely the cause as this setting gets reset to Normal on each power cycle, but check it anyway.)
4) Re-Upload your existing ARC solution. No need to re-Measure; just double click on the file where you've saved the solution and do an Upload.
5) After that, go into Setup > Level Calibration, set the Test Mode to Manual, and scroll down through the lines to make sure audio is coming from the correct speakers for each line. Better yet, play an audio calibration test track, such as the LPCM Channel ID 5.1 or 7.1 track from AIX Audio Calibration, Blu-ray. The difference in playing the test track is that it gets processed through ARC. If you hear a substantial level difference for any of the speakers, you need to check your amp next. (Do that by swapping outputs on the back of the D2v to see if the problem stays in the same speaker (problem in amp or speaker) or moves to the other speaker (problem not yet figured out in the D2v).
If this doesn't fix it, and you can't demonstrate the problem as being in the amp or speaker, then your D2v likely needs service.