Thank you both for the replies! rgardner, no I do not have the hang the joists of the floor above selected, but i did double check this after you said, because it is behaving like that. Ridge_Runner, I am attaching the plans as I am still stumped. I had to zip the file up as it is a 60mb file. I also added a picture that better shows the issue. In one room the right hand side has the floor joists in the wall framing as I would expect. but the left hand side has the joists butting against the wall with no support at all. I know I will have to modify the framing a bit to suit my needs but i was hoping that i didn't have to do this by hand. I am more worried that i have a setting wrong or something.
-Ty
ChiefUserTyMN.zip