Toby,
I believe there is an error in the "factory reset" that mistakenly defaults menu
#020 SYS FORMAT to 0000 - 1080i mode rather than 0001 720p mode. Try changing this.
The deck does not per se have a frame rate mode but plays back all tapes at the same speed; it is a function, as you well know, of the flagged frames which tell the FCP what frames to "pull-out". This frame rate setting is, I believe, a function of the FCP setup.
Good luck,
JS