Re: Strange Navigation Bug
Modifying $wp_filter and all those other vars is dangerous. These are wp internal vars that control the flow of function calls when wp does do_action() or apply_filters(). Changing their values can lead to unpredictable behavior.
Danger Will Robinson.
If you want to change the sequence of the actions and filters in wp or replace them with your own functions, there is a way to do this. remove_action() remove_filter() and the action priority parameter.