2 Modal Pop-up extenders no working on form with AJAX

Hi,
I had a web form with 2 modal pop-up extenders that was working fine until one of my co-works converted the entire application to use AJAX. Now the page doesn't load at all. If I comment out one of the pop-ups all is fine. I have seen some articles that say go without AJAX and JavaScript, unfortunately in our new architecture that is no longer an option. So I'm hoping someone can tell me how to get my two pop-ups working again.
I'm including the code for the pop-ups below if that will help:
<asp:ModalPopupExtender runat="server" ID="mpeCancellation" PopupControlID="pnlCancellation" RepositionMode="RepositionOnWindowResizeAndScroll" CancelControlID="lbCancelNewAssessment" TargetControlID="btnDummy2" BackgroundCssClass="modalBackground"> </asp:ModalPopupExtender> ...