The redefinition of _toggleChecked in jquery.multiselect.filter.js seems like overkill, particularly since the difference from the default definition is small and the behavior difference could just be handled by some sort of flag that the filter code sets on the main instance to cause the difference in logic. Right now, you essentially have to keep the two definitions in sync if any changes to them are made.
My thinking is that the flag could either be set via a new call back that the filter code calls on the instance, or a new "filtered" parameter could be added to _toggleChecked that the filter code makes use of via "currying" the function. (baking in the parameter value when filtering is in use)
Your thoughts?