Once I figured out how to properly tension the belt so it will remain centered on the pulleys, it has worked fine. It is interesting though that the belt tension seems critical on some setups and not on others. We have friends who ride with the same setup and the tension seems much less critical for them. Our bike was delivered from Co-Motion with the belt drive so I know it is not a design problem. The pulleys are in perfect alignment with the eccentric centered in the bottom bracket. I think it has more to do with the belt/pulley interface.
The bike shop that built our tandem did put the stoker's pulley on backwards. We rode the bike that way for probably 2K miles before I discovered (through this forum) that it was installed incorrectly. Co-Motion replaced the belt (at Gate's recommendation) but would not replace the pulleys. I wonder if running that pulley backwards for 2K miles may have worn it in a way that makes our system more sensitive to belt tension? If and when I upgrade, I will most likely go with the new center-track system so I will probably never know for sure.