Are you scanning straight into Acrobat, or are you opening scanned images and converting them to PDF?
Acrobat "optimizes" images when you import them. On the preference dialog for e.g. the TIFF import settings, you can select how you want to image to be processed, and one of the steps is to enable (or disable) the deskew feature.
When you use the "Optimize scanned pages" feature, you can also turn deskew on or off: