I've had the issue.  After spending a ton of time getting the alignment to work, things were great for about 4 months.  Lately, QB keeps changing the format of how I view checks (PDF, browser, Adobe)  It has changed so much I have a log jam of post it notes to help it fit (whether, fit to print, shrink to fit, default, or no scale or whatever) - it's a major pain the A$% no printing checks that align...