Dear namibian,
To update MainContent panel asynchronously, please add a regular ASP.NET UpdatePanel into it. (Looks like you've tried this)
We took a look at the live demo of ThinkGeo at http://websamples.thinkgeo.com/webeditionsamples/ and thought it might work with UpdatePanel. In the demo, under Samples -> Getting Started -> Add a Popup, the map lives inside an UpdatePanel.
Could you successfully display the map without any ZettaCube controls, i.e. with only an ASP.NET UpdatePanel and the map in the page?
Could you please send us the URL of the page in question, and the corresponding .aspx + .cs files for investigation?
Thanks