Dear Lucas,
I got an early response from WCT team. One of the possible issues is that the FreeMASTER communication is switched from SCI serial to JTAG/EOnCE port. Please check the freemaster_cfg.h file for settings.
It seems that in WCT1012 package, the JTAG was set as default:

While in WCT1013 package, the SCI was selected:

So as the first experiment, try to use JTAG/EOnCE port in FreeMASTER. Make sure to disconnect the CW debugger session first. Then run the FreeMASTER, go to project options and select this plug-in:

Press the Configure Button and see if you can get anything else than "Unknown" as in my case (I don't have any board connected). You should see the on-board debugger probe detected.

You can press Test Connection to see if the board replies.
The second experiment could be to change the freemaster_cfg.h configuration: set the FMSTR_USE_SCI to 1 instead of FMSTR_USE_JTAG.
Regards,
Michal