I guess you might be using AsyncPostBackTrigger with update panel.
which causes the partial post back and as in partial postaback complete DOM does not refresh. so your scripts would not be working.
Well You can cop up this issue in two ways.
1- inject scripts from server side
2-using javascript
function pageLoad() {}
YOu can wrap all your scripts inside
function pageload()
{
}
REFERENCE LINK: How to have a javascript callback executed after an update panel postback?
and hope that will work. :)