I'll be sure to help you align the checks when and printing issues in QuickBooks Online (QBO).
To fix the issue you're having right now, you can clear the stored cache files of your browser. The saved cache can get corrupted and damaged over time causing issues when printing checks in the program. Once done, print a sample check again. If the same thing happens, let's update your Adobe Reader and set it as your default PDF viewer. This can also be the reason why you're experiencing printing issues.
Here's how:
Click on the + New option and select Print Checks.
Select the Print setup and then choose No, continue setup.
Hit the latest version of the Reader link so you'll be routed to Adobe’s page. From there, download the latest version of Acrobat Reader.
Once the installation of Acrobat is done, get back to QBO. Then, click the How? link to set Adobe Reader as your browser’s default PDF viewer.
Next, go back to QBO and choose View Preview and print sample. Then select Print.
Follow the on-screen steps to finish printing your sample check.
Then, print a sample check to verify if it shows the correct alignment.