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FAT 16 is just listed at "FAT" when you format the drive. And yes you do just want FAT.
I found compact logger was pretty touchy about cards. For it start it only liked small capacity cards....REALLY small capacity cards....I think 128MB or so was about the limit. I bought a batch from a bargain bucket in a zoo!
There should be two files on the card -
complog.mod
Complog.pcf
I also remember the card prep program version being dependant on the logger firmware version.
Apart from getting it to work with Pi Toolbox, that is about all I can remember.
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