Hello...I was having the same issue today...ran through all the "fixes" in the Hub Tool and everything we could find in this issue string and were still getting the 2-part forms.  Our Internal IT found that there was someone that said you should reset the updates...then run updates again.  We went through that process and I'm now getting the correct 3-part form for 1099-NEC. 

So, if you're still having issues, try the Reset Updates process.  Before you try this reset update, make sure that you clock Mark All on the Options tab so you are sure to get everything. 

I hope this helps!