I setup a new Rails application using Capistrano earlier today and hit a fair number of odder than normal Capistrano issues. The biggest issue was around the asset pipeline and the asset manifest not being created. The error message revolved around "cannot stat (pathname) manifest file".
Digging into the issue with Google revealed that it actually is a problem with Capistrano itself. Here's the thread. Upgrading to at least Capistrano 1.1.8 fixes this problem.