Clause variables changed during Word sync import

I created a clause containing 2 system defined variables. After import from Word xml (configured for MSWord sync) to create a new clause the variables appear correct in the text window and both show up in the variables list. After save/exit OR apply when the clause is reopened the first variable listed now appears in both places and second variable is gone. Any ideas?

Added for clarity:

 

After clause import and 'Save'

   

After 'Apply' and re-open clause