Well my problem is solved, but I still cannot explain why. The pad was on the top layer, instead of multilayer as I intended. Changing to multilayer and re-generating the gerbers sorted it. I would have thought though that it doesn't matter what layer the pad is on, so long as a hole size is specified.
The Protel programmers didn't anticipate that you'd have a surface pad with a hole, it seems. If you want a pad only on one side, I think you use a multilayer pad with a padstack.... Surface pads are supposed to live only on one layer. Really, the program should lock you out from doing it the way you did. In other words, if it is a single-layer pad, the Hole size should be greyed out. But it isn't.
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