Sorry f/the delay, let's see how can i help you.
First, take a look at source code of your page (exactly speaking, at the part where your scripts are loaded). Are they really nested? If yes, there's something wrong with script loading template.
Go to Head.tpl and check if the following line exists:
<$PageModel.Scripts:Links(script = "true")$>
This line gets PageModel.Scripts collection (which is populated by .js files in your scripts folder) and applies Links.tpl template to every item in it. This line also passes script = true param to Links.tpl.
Second, take a look at Links.tpl itself. Among other if branches, you'll see the following:
<$if(script)$><script type="text/javascript" language="javascript" src="<$it.Path$>" id="<$it.Id$>"></script><$endif$>
It first compares if script param is true (as we passed it in Head.tpl), than outputs a script line loading javascript and closes(!!!) the tag.
Maybe you've changed the files accidentally?
Further reading:
http://help.wildapricot.com/display/DOC/CSS+and+LESS
http://help.wildapricot.com/display/DOC/Template+Engine+Reference+Guide
http://help.wildapricot.com/display/DOC/Theme+files+language+syntax
Feel free to email me your website address, so we can find the problem out personally.
Theme Evangelist