When printing from Acrobat, do you select the paper size from the Properties dialog (accessed next to the printer name in the print dialog)? Or are you checking the Choose paper source by PDF page size option?
If the latter, there is a known issue, especially for PDF files with mixed page sizes. If you don't have mixed page sizes, use the Properties dialog to set the paper size through the print driver and see if that fixes the problem.
- Dov