I feel your pain, having surrendered voluntarily to the rental agencies' various toll collection schemes (including Hertz PlatePass) and even then getting hit with defective tags and unexpected charges.

MA EZPass transponders don't beep, so that's not a reason to worry in and of itself. However, the tolls definitely would have appeared in your account by now if they were going to. With few data points out there on how the MA all-electronic-tolling works, one can speculate that perhaps the computer system read both, detected a discrepancy, and decided for some reason to go with the plate account? It also seems that MA has a difficult time sending bills to motorists outside the New England states - unlikely in your case, but you never know...