Just upgraded to SA 2.61 from SA 2.55 and it appears SA 2.61 is not reading or following the whole local.cf as it should.
I'd start off by running spamassassin --lint and fix the errors.
# Enable Bayes auto-learning auto_learn 1
Like that one.. The proper option is bayes_auto_learn 1
Syntax errors in your local.cf can cause SA to dump the whole file.
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