Without seeing the JQuery you are actually using it is difficult to be certain. However, a common problem is not taking into account the name mangling that occurs with ASP.NET.
For example, if you code was
$("#some_element_id")
This would find the element
<input id="some_element_id" />
but when the attribute runat="server" is used ASP.NET will prefix the id of the rendered element depending on the container it is in. So it will be something like this
<input id="ctrl_001_some_element_id" />
Now the JQuery selector won't find the element because the id is different. A way around this is to use
$("id[$='some_element_id']")
which will select any element who id ends with some_element_id, regardless of the prefix.