I appreciate you for coming back and to confirm that the issue about the 1099-NEC alignment also does not work in QuickBooks Online version.

Yes, the provided troubleshooting steps above are for fixing the alignment of the 1099-NEC in QuickBooks Desktop. However, if the issue continues to occur, I recommend contacting our QuickBooks Desktop Support Team. They have the tools to check your account and investigate the cause of the issue. Please follow the steps shared by BettyJaneB on how to reach them.

On the other hand, I suggest using another updated-supported browser when creating and filing 1099. This way, you're able to verify if the current one you're using has issues. 

If the issue persists, you can go to the Fine-tune alignment page so you can make any changes on the lines or do horizontal and vertical adjustments to the form alignment. Let me guide you through the steps:

1. Click the Expenses menu then go to the Vendors tab.
2. Select Prepare 1099s, and click on Let's get started/Continue your 1099s.
3. Review or enter the company name and address and the Tax ID then select Next.
4. Choose the box for payment types you made and the expense account you use for these payments then select Next.
5. Review your contractor's information and select Next.
6. Select Finish preparing 1099s.
7. Select Print and mail.
8. Go through the steps in the Select a form type and print a sample page, then select No, it doesn't line up. This option will direct you to the Fine-tune alignment page where you can make horizontal and vertical adjustments to the form alignment.
9. Go through the steps in the Select a form type and print page. Once the form is aligned, click Next. 
10. Click Done.

For additional information, I'm adding this article for more guidance: Create and file 1099s using QuickBooks Online.

You might also want to read this article to learn more about 1099-NEC filing: Set up QuickBooks for the 1099-MISC and 1099-NEC forms.

Please feel free to reach back out if there's anything else you need help with concerning 1099. I'm always here to help.