Chris I had the same issues as you when I tried to update the software, I also had to revert back. I use these settings with a Spektrum voltage protector and I have not has any issue since. But just to be safe last week I installed a castle BEC so I can run the 3.5 SP which still cogged. With the Ballistic 4.5 it's a non-issue.
bec 6 volt
arming time 1sec
dead band small .05ms
start power low
timing 10*
smart sense
cutoff 6volts
reverse lockout
brakes 75%
drag brake 0
punch control 0
reverse throttle 50%
Before the editing of my settings
With a Tekin RS Pro (had heat issues 2 weeks after I got it installed)
And my current setup (this was before the castle BEC but with the settings above using a voltage protector on the default software).
All the guys on the team use the same setup, MMP and either a SP 4.5 or Novak 4.5 (none of us had BEC's)