I have had the same problem. I set all my aterm properties in ~/.Xdefaults (with settings from ikaro's fluxmod site). One line sets the geometry of the window:
ie. the aterm is meant to open 80 columns wide by 35 lines deep. However when using fluxbox 9.6, if I changed the size of the aterm window and then set it to remember the window size, I would get the broken output in vi that you mentioned. The window was opening at whatever dimensions I had set it to remember to open at, yet aterm still thought it was meant to run at 80x35, so the output was garbled.
The solution in my case was to delete the remembered settings for the aterm window, and let aterm start with whatever dimensions were set in .Xdefaults.