For most DAWs, the Pro-Codec and Codec Toolbox can detect the number of channels and adjust the available codecs/settings accordingly.
Some DAWs don't broadcast this information, causing them to default to surround mode. You can tell when this has happened, because the input meter will show six channels!
Since the MP3 codec isn't supported for surround input, it won't show up in the codec selector.
This issue only affects the VST versions. If your host supports Audio Unit (AU) plug-ins, you can use the AU instead.
Click the Sonnox button and, under "Channel Configuration", select Mono or Stereo.
Right-click the input meter and select the Switch to mono or Switch to stereo option.
Permanent solution for REAPER users
If you're using REAPER 5 or above, you can enable a per-plug-in option which permanently solves this problem.
- Open the FX Browser by clicking the FX button on a track, or clicking the Add button at the bottom left of an FX Window
- Find the VST Pro-Codec or Codec Toolbox in the list
- Right-click and enable the option Inform plug-in when track channel count changes