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Do we only need the new palm binary, or a whole replacement Empire as well?

Just the Palm binary, the only difference is the dynamic input area support.

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But I am rapidly getting tired of the little pop-up at the end that repeatedly asks me if I want to waste my battery power for no good reason.

Your option to receive beamed data is turned off. Do you want to turn it on now?

Any chance of getting rid of that, or at least having it remember that I don't want to waste batteries?

I can't see a solution to this one. This is a Palm internal message that will pop up when you use the IrDA functions but do not have Beam Receive turned on. The only way to get rid of it (as far as I can see right now) is to turn Beam Receive on.
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Mark Cushman