That dang things been buggy since day one, I wish they'd completely re do it and get some professional help.
Every time I use it I have issues so I stay away from it for a few months each time.
I too just had to re install to get it to work when I wanted to just do one simple thing, update Cakewalk..
But if I remember the process was kind of sketchy.
I'm pretty sure I logged out, deleted it from Programs and Features.
Went to the Band lab site and had to dig around to find it, re installed and logged back in. Finally after all that I managed to update Cakewalk.
I don't miss the Command Center but this is a even bigger PITA.
Not sure what is causing your weirdness, but you might have to do a complete clean install.