I have a similar issue to print a single vendor check in Quickbooks Desktop. Very frustrating. We had a old HP printer p2035n model which worked fine before, but the printer was too old. We just replaced the printer with a new Brother HL-L2320D printer. We followed the same drill to set up the custom paper size 3.5" (width) x 8.5"(height) to fit the single check size. When it printed, the whole thing shifted to right hand side instead of left hand side "from pay to".... I tried all the settings that I could find in the support sites... did not work, scaling to the custom paper size. Try to align options, but no worked too. Very frustrating. Spent many hours research and could not fix the misalignment problem. Please help!