I have been experiencing this as well. I also have noticed the new quicktype section of the keyboard will cover the latest text bubbles a lot of the time, so I then have to scroll down to see it.
I have been facing a lot of issues in regards to screen position/orientation since I got my 6 plus on launch day. I am thinking of possibly doing a fresh install of iOS 8 if the 8.0.2 update doesn't fix these issues.