I've always used /opt/zimbra/conf/spamassassin/local.cf as the place to make those changes, rather than the file you mention; however, as I understand it either should work. I don't know why your whitelist is not being parsed properly. However, we'd know a lot more if you would post a header (at least the X-Spam portion of the header) from a message that is being misclassified. Then we could see exactly what is causing your message to be marked as junk in the first place.
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Cheers,
Dan
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