It strange that the Airport Scanner wouldn't find .BGL installed by AI Traffic packages, because they ARE AFCADs!
I'm not familiar with Traffic X but, maybe, if it *replaces* default AFCADs, it's possible they won't be flagged as duplicates.
In that case, your only option is to find the relevant file and manually remove it or, better, restore the MS default. The AI *WILL* work just fine using our own AFCAD, but having a modified AFCAD, but based on the default one, will create all sort of issues like double objects, default buildings popping out etc.