adding runat=“server” changes the behaviour of the layout

Answer 1

When you add runat="server" to a div, the system automatically generates the ID for it. It's referred to as ID mangling. Unfortunately there isn't much that you can do in the 2.0 framework for divs that I'm aware of (without it being a pain anyway), but in 4.0 we're getting an override... On custom controls though (in 2.0) you can override the ClientID and UniqueID fields. So if you created a MyDiv class that used the div as a base and then created the ClientID/UniqueID fields you should be ok.

Your other option would be to update your CSS/javascript to use the mangled ID. It's fairly static based on the position within the page as ASP.Net uses it to find a control during postback.