Note that jquery and jquery UI are loaded already by our ScriptLoader control which does not support adding your own files, so I suspect you mean you are using ScriptManager to include your custom files.
Make sure anything that depends on jquery is being included after the jquery files (view the source of the rendered page to check). If the ScriptManager is loading them before the main jquery files you may need to add your scriptws using a UserControl which you can put in the layout.master after the ScriptLoader and inside the UserControl you can add scripts with code like this:
"oomph", "\n<script src=\""
Note, the best way to easily find out what is going wrong is to use Firefox and the Firebug plugin which can show you where script errors are happening.
Hope it helps,