I'm having the exact same issue (I'm holding off from purchasing until I can find a solution).
Below is a screenshot of my current rule. What I want to do is to move
only files with the extension pdf. At the moment the rule is moving the subfolders as well as the enclosing pdf files (even if the folder also contains files which do not have a pdf extension - and they get moved too along with the pdfs).
Mac OS10.8.4 with latest software updates.

There are perhaps 2 options which could possibly be included in a menu for the move;
1. move specified [file(s) without enclosing sub folder]/ [specified folder(s) with any contents] only.
2. if search returns file types, move specified file(s) along with enclosing sub folder(s) > with warning/error dialog if folder also contains unspecified files. [if error dialog, an option to copy the file results to the specified 'move to folder', leaving the original folder and contents untouched]
I can visualise times when all these options would be very useful when sorting files/folders.