...okay...you can do that also(turning by 90°degres)...
...but in my oppinion only problem you got is to avoid excess light that is coming from not covering top of scanner properly.This you can fix with just simple trick;
-when you put swatch in scanner,close tha scanner lid(top cover),and just put one dark fabric shett ono scanner...just to cover scanner wiche will result as light isolation for scanner.

Simple and resulting...let me now did you have any succes.
Good luck!