I started a putty window, changed the font, and then did Windows-Left to fit it to the left side of the screen and it decided to do the screenshot below. The only way i've found to make it go away is the log off/on but that's obviously impractical and doesn't fix the problem.
I've had it in the past but not this bad. It usually happens when I move or resize the window. Is there a setting to have it just auto resize by default?
[edit] and then, about :05 later out of nowhere, it popped away. I'm just sitting here doing something else and it changed back to normal.
That means that you (or someone else) is connected to the same Byobu session from another computer with a smaller terminal size.
You should be able to kick the other session using Alt-F6.
Full disclosure: I am the author and maintainer of Byobu.