Thanks for the comprehensive reply.
I'd made sure it was stand alone, there is a window manager on the page but not attached to this window. I get this isuse appear before any post backs / ajax calls so had ruled out that being a cause.
I think I'll have to make a test page.
Good question re the content page. Essentially I now have just one page on my site and each page is dynamically generated from class models. It gives me great control over how the site works and I will be able to make changes to the base mechanisms a lot more easily. But the setup is more complex. The page in question is a dashboard style page where I want a filter popup window. I could make it so that there is a mechanism built into the page to display the filter as a sub page I suppose - but it would probably increase the complexity considerably.
I'll create a support ticket if the test page doesn't tell me what is wrong.