I still had the problem for a few days until I discovered that Win 7 is hiding the folder where they neede to go. My fix was this:
Locate the Programs folder, copy, and paste into the Rapture folder.
Open Rapture, click on the Save As Icon to open the hidden folders in Rapture. DO NOT MAXIMIZE THE WINDOW!
While that window is open, go back and right click on the expansion folder you want to move and click copy.
Go back to the open window and right click copy into that location.
Repeat for the next expansion folder.
When all is done, close Rapture. Re-open it, click on the library browser, Press F5 to re-scan and it should show your new programs and folders.
I had to fiddle with this for two days to figure it out but it works. I hope it does for you.
The problem is that when you just use Windows to browse the folders in Rapture, the hard drive does not show the folder you need to be in to drag and drop the folders. I'm sure there is an easier way, but I couldn't figure one out. Let me know if it works. I admit it is confusing to read. Try it and if you have no luck I will try to figure out a more in depth way to explain how to do this.