Thanks all for your help.

I think I made a couple of mistakes, or wasn't clear, in the first post.

Yes, dws, the question is "what causes the client to time out", and the client is, unfortunately, the script being run by AvantGo that I have no control over.

But in answer to your other points, I did have $|=1; not zero, (mistake in posting, not scripting) and I did have little bits of output dribbling out as the script progressed to try and keep the other server interested.

My "when does a web server know the script is finished" question should have been formulated "my web server seems to be signalling somehow earlier to the AvantGo client, in the new version, that it's finished, which doesn't make sense because it actually finishes, if anything, later than the old version, it just stops outputting HTML earlier."

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Weaselling out of things is important. It's what separates us from the animals ... except the weasel.