I'm using Mobile Safari's cache manifest file to store a multi-page data entry application that is run on an iPod Touch (version 3.1.3) in offline mode. The application writes to the client-side database by way of the persistence.js ORM. This all works fine.
However, I run into the occasional, extremely hard to reproduce problem whereby Safari just seems to forget that the pages are cached. When this happens, the "Cannot Open Page" alert appears, which is the same one that comes up when you attempt to visit a non-cached website with the wi-fi turned off. The only way that I've found to fix this is to reconnect to a wireless signal and visit the site while online, which seems to set the cache straight. This is easy to do when you're in the office, but not so easy to do out in the field.
I'm not trying to reference anything outside of the cached resources, and I've verified that the application is cached by running through the entire site while disconnected, sometimes successfully for days on end. I feel like there's a bug in the OS that messes with the validity of the cache. I'm not necessarily looking for a solution to the problem (but that would be nice), but rather just some confirmation that others have encountered this problem.