An iOS 6 iPad app shows content in two UIWebViews. If both web views contain a jquery image rotator, only one will work at a time. Running < iOS 6, both work properly.
JavaScript works in multiple UIWebViews but it depends on the JavaScript. Using JQuery or other external JavaScript code can be a problem in case you link it with a href. You can solve these issues by copying the code of all external JavaScript libraries into your web page HTML. This is the reason why simple JavaScript works fine. Example:
This is a UITableView with a UIWebView in every UITableViewCell. In webViewDidFinishLoad i do [webView stringByEvaluatingJavaScriptFromString:@"document.write('hey hallo'+new Date().getTime())"];