I think one thing you can try is disabling WMA from the encoder setting by editing settings file. But I'm not sure this can fix the issue or further action is required.
Anyway, open MusicBee3Settings.ini file with a text editor and find
Then two lines above it,
find "<Enabled>true</Enabled>" and change it to "<Enabled>false</Enabled>".
Save and restart MB.
If this doesn't help, then ask Steven for help.