I assume you are using an external DTS decoder (usually a HT receiver).
1. Use a sound card that can pass through unaltered audio stream to SPDIF and has ASIO support. If the files are 44.1 kHz be aware that not all sound cards can handle 44.1 kHz audio without first resampling it to 48 kHz. The Windows kernel mixer resamples automatically when needed, but in this case that would corrupt the DTS encoded signal. ASIO is way to bypass the kernel mixer completely.
2. Use the ASIO playback mode in MJ and disable all digital signal processing (replay gain, internal volume, DSP effects, resampling etc.). MJ will decode the FLAC files to unaltered PCM and your external DTS decoder will not see any difference when compared with direct wav playback. It doesn't matter if the PCM signal is stored in a wav container or if it is compressed a bit by using the FLAC codec - the decoded output is identical.
The above should work on XP. Vista may be different.