Ok, taking a step backwards.
After the balancer install, was your timing even off? For a straight balancer swap (where the old one had not slipped. and the car had not been timed with a slipped balancer), the timing should have stayed the same/been correct. They keyed interface between the balancer and crank accomplish this.
Did you have to change the timing much after the install? If it was off by a lot, were any of your TwEECer settings dependant upon having had a bad timing reference? Like your timing tables were way off to accomodate a slipped balancer?
The global spark stuff in the TwEECer is ok?
Just random things that are coming to mind. Since this happened after the balancer install, it's gotta be something that was touched/messed with during that time.
Good luck bud.