I have a page with some controls, usercontrols etc.
when I change a div from plain
<div id="foo" runat="server">
If you're targetting the ID of the div control in CSS and then running the control at server, you'll find it no longer applies the style.
This is because ASP.NET has a built in mechanism (INamingContainer) to ensure than you don't have multiple controls named the same. It does this by adding container prefixes so you end up with:
<div id="ctl00_ctl00_myDivName" runat="server" />
The easiest way around this is to change it from working on an ID to working on a class:
<div class="myDiv" runat="server"></div>
Alternatively, I believe that XHTML requires that Divs have closing tags so use
<div runat="server">Some content</div>