What you could try is to enable the stereo encoder in Stereo Tool - but that will only work if you can disable the stereo encoder in the transmitter.
May I also add, if the stereo coder is on a separate board to the main TX (as many are), it's not enough to bypass the stereo coder, but to also disconnect any power feeding the stereo coder as well. I had major sound defects after bypassing the stereo coder (running MPX), but all went away after I disabled the stereo coder power as well.
RadioDJ 188.8.131.52 | Stereo Tool 9.90 | MBRecaster 184.108.40.206 | Aareff TX
The ONE - 107.3FM Whakatane, New Zealand | www.theone.net.nz