Once you hit a form post action (like the submit button), the browser will very likely "lock up" until it starts receiving a response from the server. I don't know if there's any way to avoid this.
I have notice a slight difference in behavior between my work computer and my home computer when running AJAX type of actions. My home machine which is running a slightly newer version of MSIE updates graphics and such while an AJAX call is in progress while my work machine doesn't. This might be due to any of three major factors:
1. Home machine is newer version of MSIE
2. Home machine is connected via VPN and thus a slower network connection (maybe the network lag is enough for the browser to do what it needs before the AJAX response shows up)
3. When at home I'm 'talking' to my development machine at work via the network, where-as at work, I'm 'talking' directly to the same machine. Maybe the fact that when I'm at work the same machine is doing everything: making the request and serving the response. However, I have seen the same behavior from another work machine (which is running a similar version of I.E.).
Despite all this babble, I suspect that the most likely cause of this problem is that the form post is stopping all other browser activity including those timeout calls.
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Peter