Answer:
It is because of section ID 5. The value of B4 is changed to 0 to 0.005 which is the half thickness of the web. 
Before change.
After change:
As shown in the images above, the bottom flange should be long enough so that the end of the flange should be connected to the centerline of the web. This error check has been added from Civil 2019.
Two modified files are attached here.