Hah. I come back to this thread once again, after figuring it out weeks ago then losing my configuration.
I got DTS-FLAC files playing in WMP and MPC using madflac as my flac decoder and some sort of configuration...with ffdshow I'm assuming. I since then re-installed a whole lot of filters/codecs and put them back on, have had a thorough look at them for conflicting filters and am stuck.
Can anyone shed some light? The flac decoding's fine, but it will not find the DTS and process that.