The dual SCT folders in http://www.wowace.com/files/ apparently confuses WinAceUpdater. It tried to update SCT/sct twice and I ended up with an sct folder that contained no extrenals. It is not unique to your addon either, Autobar/AutoBar has the same problem.
I have somewhat the same problem. it just seems to check the SCT and then skip sct & sct_options. When I uncheck SCT it works like a charm though :)