I’ll post some general info here and then PM you for the details.
A timeout happens because onLoad (Document Complete) didn’t fire before the test timeout period (1 minute). It is usually caused by some code that confuses IE into thinking it isn’t done or a tight loop that prevents the event from firing. We have seen the problem at times when using the addthis widget (with their flash code enabled IE always thinks it has one remaining object to download).
It can also be triggered if the network activity never stops (because of a polling request or something like that). That’s because in the default testing mode Pagetest wates for 2 seconds of no activity after onLoad before stopping. You can force it to stop at onLoad by checking the “stop at document complete” box in the advanced settings.
You can get a hint of what is going on by going to the screen shot page and look at the browser status messages. It will tell you if the browser thinks something is going on at the end of the test (like if there are items it is still waiting for).