Box 1 Loss from a K-1 is not showing up on Sch E Part II even though disposition of the partnership & Investment at risk are marked YES.

Go to the upper right hand corner and select "FORMS"

Scroll down and select your K-1 with the respective partnership name.

Scroll down until you see "FINAL K-1" and click on the box next to it.

That fixed my problem.  Hope it helps!