I tried to fix this 3 per page issue by doing the program update on my own but ended up calling them this morning and they walked me through the update. Customer service number is 800-446-8848.

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

2. Log in. Help>Update QB Desktop>Update Now. Make sure ALL boxes are checked off. 

3. Click on  'Reset Updates' > Get Updates.  Once update completes, close and restart QB.

4. Restart your computer to install updates. Login to QB.

You now should be able to print 3 to a page. 

Go to file>Printer Forms>1099/1096

Make sure to Map Vendor Payment Account by selecting NEC Box 1. 

Best of luck. This was frustrating to be sure & I'm glad it's behind me.