I have been using the sheet set manager with very few problems for years until - you guessed it - I was upgraded to Windows 7 OS v6.1 and Civil3D 2012 IDS.
Up until then, I was able to open layouts in different drawing files through the sheet set manager while in an open file. Now, I get an error message (see attached) and have to close the file I'm in to open the other.
I can open files through the regular file open command and have more than one open at the same time, but it takes away the convenience of using the sheet set manager to avoid having to browse to the desired sheet layouts when copyclipping sheet layout drawing elements from one file to another.
I have studied every sheet set system variable to see if that was the problem, but could not find an answer. I have the same problem in Civil3D 2010. It happens to new and existing sheet sets in both versions and sheet sets made before the Windows update.
Given the few posts I've seen on this topic, I assume that either there's some kind of acceptable fix, or it's not happening to anyone else.