When using the GUI, have it generate a CREATE script for Database A, a CREATE script for Database B, a RESTORE script for Database B, and a RESTORE FILELISTONLY of the backup file. Show us all of this and there will be an answer in there somewhere.

The only thing I can think of is if you detached Database A, and Database B had files pointing to the same location. You restore B without a WITH MOVE clause and it overwrites A's files.