I have tried but cannot reproduce this problem locally, the only differences I can see between your setup and mine is that I am using Eclipse 3.2 GA and not the RC7 release and I am also using a new workspace. (Also you are using MyEclipse to do the deployment and not a custom Ant script correct?)
Let’s try a new workspace to see if that helps:
File > Switch Workspace > C:\tempworkspace, hit OK
Now create a single new web project with a single default JSP in it. Setup the Tomcat 5.5 connector and deploy your project, set a break point on the line at the top of the template that computes the basePath and run the page from your browser. First, does the break point have a little check mark in it when you set the break point? And secondly, when you hit is, is the source shown?