There has ben quite a bit of discussion about this, so I'll put forth my direct experience to hopefully clarify the situation.
I had received a notice quite some time ago and was never able to get through to them by the time of the deadline (several months ago.)
The problem was they were trying to match a plate number I had decommissioned several years ago.
Just a few minutes ago, I looked for and could not find the letter. I called anyway. The nice person on the other end of the line was able to look up the violation and clear it up (removing the fine and charging the toll to our account) without any difficulty. The whole thing took about ten minutes.
So, there is never a reason to go through a manual lane to avoid the chance that a transponder will not be read. A fellow member broke his leg when he did just that and slipped on the build up of car snot in the middle of the lane. I felt bad for him and I understand he did so because he thought these things were impossible to deal with. There were certainly difficulties in the past which were widely reported, but apparently the Toll Authority has hired a better contractor

and the process is now relatively painless. Incidentally, I called at about 6:00 PM and waited about a minute or two to get through.
I hope this helps someone else avoid needlessly going through the manual lanes due to possible transponder difficulties.
-hank