or create a photoshop action and do it just once in Photoshop. After that just batch script stuff inside Photoshop (file > automate > batch processing or something like that once you have your script recorded).
photoshop cs1 or photoshop 7 - you can easily get fairly cheap LEGIT ones from ebay. I bought my photoshop 5 off ebay for about 40 quid a year and a bit ago.
I just tried doing this as 2D shapes in Photoshop and as 3D shapes in Modo and baking out normals and AO. The 100% Photoshop method was faster and easier. It'd be a cinch to get normals from the shapes in Photoshop, too.
If photoshop is still open, there is no way around it. You have to close photoshop for it to release the lock. Now if its happening even with photoshop closed, I'd use WhoLockMe, and kill the offending process. http://www.dr-hoiby.com/WhoLockMe/
I tried to bake 16 bit full float with Knald, and the result is even more weird. :'( Tried to bake with Xnormal 16 bit rgb. Unfortunately there is no option to bake it in grayscale, at least i didnt find it. Map converted in gray scale in photoshop