OK, I've narrowed down the issue
I have a loop in my aspx file with the following lines:
<%: Html.MakePopupForm<HomeController>(o => o.PopupForm2(0, item.ID), width: 500, height: 400, title: "Pop")%>
<%: Html.PopupFormActionLink<HomeController>(o => o.PopupForm2(0, item.ID), "Pop")%>
The Pop Up form reacts as stated above.
Also if I but the above code out side of the loop, the pop up works fine.
Finally if I leave the code in the loop and also put the code outside of the loop the pop up still reacts as above no matter what link you click on.