I am using JQTouch to create a Web App on the Homescreen using meta tag "apple-mobile-web-app-capable", but no matter how many times I clear the cache from within Settings, the Web App's Javascript is still an older cached version.
Strangely enough, if I set the meta tag's content to;
<meta name="apple-mobile-web-app-capable" content="no" />
...then add the Web App to the Homescreen, I get the latest version when I launch it.
Yet if I set the meta tag to;
<meta name="apple-mobile-web-app-capable" content="yes" />
...then add the Web App to the Homescreen, I get the older cached version.
PS. I can confirm that is only the javascript which will not refresh.
You could try adding a unique string to the end of your js include's src attribute (use a timestamp, for example). Bear in mind you'll have to change this unique string for each refresh you want to do, so you may want to consider doing lazy-loading (which may in itself solve your problem):
<script type="text/javascript" src="myScript.js?012345"></script>
This usually forces the browser into grabbing the latest version of the script. Might work...