This is perhaps related to this question, but I have slightly more information.
I recently updated an ASP.Net application to .NET 3.5 after coding a few new pieces w
My initial thought would be that something is happening where the javascript is erroring out (un-caught) and aborting the async postback.
If you can get this to happen in a development environment, you might want to try error handling the window.onerror event and throwing some alert boxes up. It might help to see where possible errors occur.