What kind of heat do you have?
Is there a door in this area?
Do your exterior walls have a slight bow on the outside. You will see this if you look down the wall. Where there are no windows or doors in the way it will show up easier.
Is there any sign of crushing of wood at these areas?
I'm on the same page as SQ Eye, I think if it is only one joist that is short it was installed short.
If a couple of joists are short then this is different.
We need some better descriptions of everything that is going on ,but I think we can at least narrow it down.