I have the same sort issue. By selecting TWAIN, use native UI, and changing the page size in there, everything works correctly. However, when I do that, I can't find a way to do bypass the dialog. I have to start a scan in NAPS, then select scan again in the dialog that comes up. Can NAPS be set up to do the long document as a predefined setting? It's not one of the options under "page size".