I had the same problems. Here were steps I took to get my 1099NECs printed correctly:

1) Close QB. Right click and run as administrator.

2) Log in. Help>QB updates>Options tab. Make sure ALL boxes are check, including 2 in the middle of page and all items at the bottom (even if you do not have a payroll subscription, choose payroll too.)

3) Update tab. Make sure 'reset updates' is checked. Make sure all items are checked as well. Update QB. Close QB when complete. 

4) Install QB tool hub and run Program> Print & PDF repair tool.

5) Restart your computer to install updates. Login to QB.

6) Go to file>Printer Setup>Forms>1099

Verify your printer name is correct. Choose align from the right side of screen. Adjust up vertically 6 for Brother Printers, 8 for HP printers. Save.

7) Run 1099 Wizard and verify your mapping is correct for your 1099 accounts. And hopefully, print your 1099 forms. 

This is what worked for me after hours of trying different things. I hope it helps.