To JohnCranberry:
I hate to be the one to say this but you're confusing the issue of volume with sound quality. Many people, yourself included apparently, feel that louder is better. However that is not an actual description of quality, just quantity.
DTSHDMA, WAV, PCM, LPCM, TrueHD & FLAC are all lossless codecs and therefore mean they have the exact same information in them and will sound identical with a properly set up sound system and the master volume adjusted so the volume coming out of the speakers yields the same decibels. Provided the source material is masted and then the same data is encoded, it's the same. The only way there could be a difference is if the audio was mastered and then encoded by say TrueHD, and then mastered again differently and encoded by say DTSHDMA...however even if it was encoded again with TrueHD it would sound different as well.
Some of those formats have metadata which trys to tell the receiver or processing unit to adjust the sound in certain ways...however this can all be voided by turning that processing off and adjusting the volume respectively.
It could very well be that your audio system just isn't good enough to reproduce very high quality sound or quality sound to the volume you would like...if STAR TREK 2009 sounds muddy then I think it's stressing out your system. On my system it sounds crisp, clear and amazing in TrueHD, DTSHDMA, LPCM and in FLAC. I've done them all. It's funny you picked that movie because I used that specific movie to do sound tests on my system. One other consideration about your system could be it's not set up just right either...possible the speakers are slightly out of alignment and your getting interference. And lastly it could be the specific sounds from that movie track are such that they bounce weirdly off the walls, or furniture in your room and make it sound muffled. All these last things can be fixed by a proper optimization of your sound system and speaker placement.
Lastly, you can't compare different movies and say that he codec is bad. If the audio sounds bad when using any of these lossless codecs, then it's either the recording and/or mastering of the audio that was done poorly, or it's your system not reproducing the sounds properly.
PS - I almost forgot to add...I like DTS-HDMA better only because it seems to be more compatible with more equipment. My Sony BDP-S590 won't play an mkv file with TrueHD, but is great with the rest of the codecs. Also, lots of software to rip/encode/decode doesn't like or won't do TrueHD where it will DTS. With that said, if you're only ever going to play a bluray disc movie in a bluray player connected to a receiver that can output any of those codecs...than I have no preference...they are all FANTASTIC!!