If there are no changes except the masterpage conversion, there could be a possible of mismatching of the control reference id.. What I would suggest is to check If you are opening the popup using $find({popup id}).show(). If so, please check if the popup id is correct. By inducing the master page the, runtime Id will be changed.
To be on the safer side, you can use the below code
$find('<%=mdlPopup.ClientID %>').show();
Here
mdlPopup is the design time id of the modalpopup Extender control.