Actually, they are about the same.
<%%> is a shortcut, but with <% and %> you can do <%=varname%> which is a shortcut for <%response.write(varname)%>. Just placing =varname on a line within the <SCRIPT> tag does not work.
Another thing is that <% %> respects the default language you set up in IIS control panel. And that the ASP parser first evaluates all the <SCRIPT> tags and then the <%> tags (NOT SEQUENTIALLY) or the other way around.. I am not quite sure which one it is.
Maybe there's something else which I don't know of... Yours,
Rob.