As this model is the only Powerbook with automatic CPU frequency scaling what are the correct preferences to use in settings?

You don't need to tweak anything really. The only thing that's in settings is the ability to disable full speed.

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I ask because running a classic Amiga app, Protracker, in E-UAE, the playback speed goes from normal as expected, to a slow crawl - as if the CPU has scaled back and the internal timing has gone wrong.

Interesting. I'll have a look at this in the evening.

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I've installed a newer version of e-uae and tweaked the config file - I've haven't seen the same slowdown since.