I had this same issue before (it showed up purple instead of red though... no idea) and as soon as I tried to reexport the model (or was it vmt/vtf?), it wouldn't let me saying there wasn't a texture assigned. Which there was.
I solved it by deleting the WWMT helper for the model entirely and recreated it, adding the settings I had before. It let me export it after that so I assuming something got stuck.
I think the $scale command in the .qc file needs to be before the reference file as it affects everything below it. Check the .qc file that WWMT generates and see if that is the case and if not, just move it before the $model command. If doing both this and recreating the WWMT helper doesn't fix it, I'm out of ideas.
I solved it by deleting the WWMT helper for the model entirely and recreated it, adding the settings I had before. It let me export it after that so I assuming something got stuck.
I think the $scale command in the .qc file needs to be before the reference file as it affects everything below it. Check the .qc file that WWMT generates and see if that is the case and if not, just move it before the $model command. If doing both this and recreating the WWMT helper doesn't fix it, I'm out of ideas.