@barrie: MT Pro stores position and size of all windows and panes... so it might be a problem with the permissions of where MT Pro is storing the preferences. It stores them in a file in a hidden folder ".Bome" in your home folder.
You can open a terminal and type this command:
If that doesn't help, here is an issue I found via Google:
By going to Finder and going under "Get Info" for my homedir, I have
gone to Sharing & Permissions and changed from Read Only to Read &
Write which seems to fix it.
Btw, we'll switch to a more common place on OS X to store the preferences.
@hellokitty: could you please clarify what is weird? MT Pro does have a somewhat unique look and feel, but we believe it's quite usable...
Thanks,
Florian