The way I handled it was to test each codeset (I did not use the internal code test) for a given device and see if power on/off worked. As I assigned keys I would test to see if the code operated (in advanced mode Add IR->[select code]->Test IR) to see if it worked. If it didn't I would learn the code via PENG.
This proved to be a pretty quick way of getting things done with a minimum of work. BTW, learning through PENG works beautifully. There is no need to learn the code in the remote and then upload the resulting PCF.
--John
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