VERY interesting. I spent two long mornings playing all sorts of different WAV files with RTA and had nary a problem.
If you need to start the player without a playlist, you can get to a shell prompt (quickly press ctrl-C before the player app starts up) and then start the player app by hand with:
./player -i
This will make it come up with no songs selected and you can select a different playlist.
How big was the WAV file in question? What was its sampling rate? Was it stereo? Maybe it wasn't that file but rather another one in the same playlist that was the problem?
Note that a test-tone WAV file need not be a long one in order to be useful. You can set the player to repeat just the one track and it'll just loop that test tone indefinitely.