Have you tried the stock HTC player? Are your files standard .mp3 files? Are they in a folder called music?
You might try one test for me. Put just one .mp3 in the music folder in the phone storage.. the rest can reside in your music folder on the SD card. I seem to remember having a similar problem and this was my fix. Don't ask me to explain why it won't look beyond the stock folder for tunes if it's empty... no clue.