Kosh - I can confirm that I see something that I believe is similar to you.
I use an HTPC to play my movies and setup playlists to show trailers before the main feature. For months, if I showed a DTS-MA trailer, and then a Dolby TrueHD trailer in succession, I would not get audio on the TrueHD trailer. The main feature, if DTS-MA encoded, would play just fine.
Very recently, I added delay of 4 seconds between each playlist item in my software used to play the trailers and movies (Zoom Player Max v9.0). Now, the SP3 seems to be able to make the switch between DTS-MA and TrueHD and I get audio in all my trailers of different high-def formats when played in succession.
Of course, there's a catch. Now I get a nasty short burst of static (undecoded audio, I assume) when the switch is made. Sounds like hell and really takes away from the "Theater experience."
Did you ever make any progress with Stan on the issue you identified, or the HDMI firmware update issue?
Regarding the HDMI firmware update, I'd really like to apply this update!! I want the SP3 to pick the highest common denominator when 2 screens are attached - I plan to introduce a 3d display to the outputs and I do NOT want to have to disconnect the 2d display to get it to work!