Were you in the UW System Design course last term? We had a couple of courses that had issues with monocleCAT, and we learnt a lot from them.
One of the biggest issues that caught us by surprise was the effect a room full of connected students can have on a lower-quality access point. We learnt from that, and totally rewrote our synchronization code to be much more robust and efficient with bandwidth (something I'd love to write a post about some time in the future).
We used to be hosted on Google App Engine, and we suffered greatly from dowtime issues that plagued every App Engine site all throughout the term. We learned from that and switched to Amazon EC2, where we've built a backend that automatically scales up to thousands of simulatanous connections.
We discovered that while most users have laptops or netbooks, few users like lugging them to every class. We learned from that and introduced iPhone and Android applications, as well as enhancing our SMS submission system to send back confirmation messages (with an easy opt-out process) for students on legacy phones.
We discovered that some professors had teaching styles that didn't take advantage of our software, so we've started being more agressive in our professor approval process, as well as introduced training sessions to help professors get a feel for how to incorproate the system in their lectures.
The biggest lesson we've learned is to find early adopters that are willing to work with you to improve your product, and to build strong relationships with them. Our product has improved monumentally in the last few months thanks to their support.
We've signed on a number of new professors in the Engineering department at the University of Waterloo, so it's quite likely you'll be using monocleCAT again next term. In recognition of the issues some students experienced last term, we'll be giving vouchers for a free term to students in the courses that had serious issues (you'll probably be seeing yours in the mail in a few weeks).
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EDIT: when I say we had a couple bad courses... the System Design course was the one that really had issues (hence my guess).