When using master pages and user controls the rendered ID of your controls change, but there is a way to stop it.
Let's say you have a Textbox
<asp:Textbox id="txtName" runat="server"></asp:Textbox>
on a standard asp page, it's id will be as you expect, txtName
Now you add a master page, called Site.Master. In your rendered html, the controls name is now different.
cntl1_Site_txtName
I might have the syntax of the new name a bit off, but you can view source and find it for yourself.
There is a way to control that though. There is a property on your page, ClientIDMode.
If i remember correctly it has 3 or 4 options. Auto ID is default I believe.
If you set it to static for that page, then you will no longer get the verbose control IDs, they will be as you expect.
This can be a downfall when using things like Repeaters though. You will not have easy access to specific fields if they do not have the verbose ID