So the new jQuery code for the filter ":visible" breaks the tablesorter's built in Zebra functionality... kind of a hacky fix, but at least it works with a minor change
at the end if the tablesorter.js file is the addWidget code for zebra, change $("tr:visible", table.tBodies[0]).each(function(i) { // existing code inside this loop }); to $("tr", table.tBodies[0]).each(function(i) { if ($.css(this, "display") !== "none" && $.css(this, "visibility") !== "hidden") { // existing code inside this loop } }); so pretty much took the selector code from 1.3 and used that inside of ":visible", not sure if that's the best fix ever, but it does make the widget act as it's supposed to