I had a similar problem after the 3.0 release. There is a script you can run (which I think they have instructions for on the download page at curse) that will remove all of the Healbot settings from your UI (there's settings mixed through different files in the WTF folder) which will completely reset everything. After that, you should be able to install and run it just fine. You will have to set everything back up again, but chances are that since you already know how you like it, it shouldn't take more than about 15-20 minutes, even if you have multiple skins--I think it took me about 20 minutes, and I use 4 different skins (solo/5-man, 10, 25, and 40).
Yea i've had those problems too. Like zeuq said there is a program you can run in your healbot folder. Curse says it's like a .BAT program (I forget the name of the file). It brings up the black command prompt and says to type "D" to delete the files. It goes into your WTF folder and deletes all of the healbot files in it. I did that and it worked again for me but had to do it again then next day when i logged in again. Seems like it works sometimes and not others. Maybe another addon is messing with it or something idk. Hope that works for you.
Also, WoWMatrix no longer can pull updates from Curse and another major add-on site I cannot think of anymore. Apparently it was way too awesome to compete w/ Curse's updater, so they banned its use.
Therefore, WoWMatrix will not update most add-ons anymore, even though it shows them as up-to-date.