A quick search on google and in the blink of an eye, from the documentation;
By default, scriptaculous.js loads all of the other javascript files necessary for effects, drag-and-drop, sliders, and all of the other script.aculo.us features. If you don’t need all of the features, you can limit the additional scripts that get loaded by specifying them in a comma-separated list;
<script src="scriptaculous.js?load=effects,dragdrop" type="text/javascript"></script>
See this page;
http://madrobby.github.com/scriptaculous/[
^]
:)
To answer your second part, there are probably javascript dependencies or naming conflicts in the libraries, and by changing the order, the javascript is being loaded and executed differently.