I was a bit surprised when I logged into the program and saw an error box which said "Your current license doesn't allow use of MSSQL database. Please use MySQL as database."

Is this a mistake?

According to your FAQ there is no difference between the free and professional edition with respect to features or functionality. Not being able to use MSSQL as a database backend IS a difference in features and functionality. Is this restriction a new one as I can't see it documented anywhere?