This is the solution that is needed. I will explain why it is a problem: when loading the server plugins are compiled into one assembly and if some plugin makes a PatchAll, it is applied to all patches from all plugins several times. Because of what plugin someone's patch used another plugin can't apply the patch correctly and work with it correctly. The problem is not in the library and the solution is to fix the problem plugins.
That you didn't get problems previously is more likely just luck and it worked up to a point. But it can happen with other plugins too, it's just that the library is extremely sensitive to the patches it needs.