Thanks guys! It was fixed by having the script add custom classes to the invalid forms and focusing on them. We tried scrollTop, but that didn't work at all, so we went with a focus scenario. The invalidHandler function code is below for anyone who's interested:
// invalidHandler to set focus to invalid controls
invalidHandler: function(event, validator) {
var $invalidElement = $(validator.errorList[0].element);
if ($invalidElement.hasClass('chosen-select')) {
$invalidElement.trigger('chosen:activate');
} else if ($invalidElement.siblings('ul.token-input-list').length > 0) {
var $inputToken = $invalidElement.siblings('ul.token-input-list').find('input');
$inputToken.focus();
}
}