FileReference and FileReferenceList in Actionscript will cause a script timeout (or rather several script timeouts) with lengthy uploads. This is a problem because Flash is sometimes the only practical way to upload a large file with a progress bar (Java is fat, a memory hog, and is not as widespread as Flash). I managed to solve this “bug” by periodically calling a worthless function in Actionscript from JavaScript, successfully “tricking” the Actionscript engine to reset its timeout. I imagine it would work from within Actionscript too, but at the time I was working with a JavaScript< ->Actionscript JavaScript library.