When I look at the flytreeview.dll in the project and in my flytree install directory, it claims it's version 4.3.1.54
Now its clear.
Starting from some version of FlyTreeView, we do compatibility tests with popular javascript frameworks.
I think that is the reason why you get issues with Prototype - your FlyTreeView version is too old (when FlyTreeView didn't contain these tests). That is why I do not get prototype issue with the current version.