I think I have worked out the problem. I was using a div structure from an existing site and was simply trying to get the header section working. However the header section included the following markup
|<div id="search"> |
| <input name="SearchCriteria" type="text" /> |
| <input type="submit" value="Search" name="submit" title="Search our site" style="font-size:.9em;" /> |
As soon as I commented out this code the problem I described was fixed.
This suits me as I needed to make these into asp.net controls anyway, but it seems that there is a problem if you try to include standard html form elements?