If the PS3 is doing the decoding and you are sending it to the amp via PCM, it shouldn't be a problem with the amp. The "DTS bomb" only happens when you bitstream to the onkyo amp and only on certain titles. I know for sure some of the titles you mentioned are ones that have the DTS bomb, like Master and Commander.
As was said above, you can do a firmware update to correct this issue. You can go here for instructions on how to perform this update..
http://www.avforums.com/forums/showthread.php?t=739501