Some users find that using the "Save to PDF" print feature in Adobe PDF 9.0 causes their systems to show a duplicate print window. While the system eventually lets users create PDF documents without errors, the duplicate window can cause confusion.
The windows may appear if you have an old version of Adobe PDF installed, which lets you use Adobe's engine for creating PDFs. While the features provided by Adobe PDF are redundant to those offered by OS X's "Print to PDF" option, some people may have installed Adobe PDF along with other Adobe products, or for compatibility reasons.
To tackle this problem, try one of the following:
Remove Adobe PDF
Go to the "Print & Fax" panel in System Preferences and remove the Adobe PDF printer option. This will prevent the system from interacting with it when print dialog are open.
Update Adobe PDF
If you need to use Adobe PDF for creating PDF documents, try updating to the latest version of Adobe Reader, which was updated earlier this month.