i agree wholeheartedly. The Leonardo is an abomination that was created to solve a problem that never really existed. Sorry if this sounds harsh but it is how I feel, and I am only stuck with one of them, not 25. I used mine for about 15 minutes and just gave up. There was/is absolutely no reason to put up with it's ridiculous behavior.
For your application, there are a lot of great boards around that were specifically designed to be used in a classroom/development environment. Like this: OMS Omega-328 SB AVR MCU Arduino compatible (Free Atmega328!) | eBay
I got one and have not looked back. It is soooo much nicer to deal with for development work than even an Uno or Duemilanove. The only thing is that it's bigger and not really suitable for embedding in a final project. Not that I'd do that anyway, but others seem to from time to time.
I know it does not help you now, and I wish I knew a way to do that, but you have my sympathies. I feel for you.