@Ashley - I'll have to do some more testing with simpler demos. (I didn't think my game was that complicated, but there certainly is about 1Mb worth of png-files (oops) and the c2runtime.js-file is 929 kb...)
I actually just now also found out that our server was serving the .appcache-file with the wrong MIME-type, but even correcting that didn't help. After closing and opening the web app a few times I lose all or some of the sounds, which also means that the Ipad has frozen.
Must do some more testing