"I'm wondering if any of the work done in the past three weeks could have set this off? Between needing new brakes and the clutch, I've put in over $2400."

B-
It is quite possible that the work they did has indeed caused the problems. I'm not a mechanic or a hybrid technician. But I own a 2003 HCH and just had my clutch replaced at 80k. The day I drove it home it had the same symptoms you describe- of having no battery charge unless you are breaking, etc. My first guess was that something they did or didn't do made it do that because I gave it to them with a perfect battery that I've never had a problem with ever.

I am really glad I found your post. I am hoping that they don't ask me for money to fix something that they did wrong. If they do I'm going to do my best not to give it to them. It sounds like this has been done before by a different dealership, so it's obviously not my fault or driving style or whatever they will try to blame the problems on this time.