not everyone is an email
expert that understands how RBLs work and that it's bad
to share a recursive DNS server on an SA server.
I will investigate this (URIBL_BLOCKED) further tomorrow (https://wiki.apache.org/spamassassin/CachingNameserver), however I doubt that it is causing the bayesian classifier to report as ham.

https://wiki.apache.org/spamassassin/ImproveAccuracy
I have gone through this wiki (and ones like it) at least a dozen times.   My server is blocking about 50% of the spam, thanks to some of the other layers of spam protection.  It's just bayes that I can't seem to get right

Why is it marking all messages as ham?

Probably because you're overtraining as ham.
I have tried the following 3 scenarios:
1.  Training SPAM only  (it's in its own folder)
2.  Training a folder with known HAM
3.  Training with inbox as HAM
In each scenario I carefully ensured that only SPAM was in SPAM and no SPAM was with HAM.  In all 3 scenarios it always marks every message as BAYES_00=-1.9.  Before each scenario I ran sa-learn --clear and sa-learn --sync

add_header all Bayes bayes=_BAYES_,N=_BAYESTC_(_BAYESTCLEARNED_-_BAYESTCHAMMY_+_BAYESTCSPAMMY_),ham=(_HAMMYTOKENS(5,short)_), spam=(_SPAMMYTOKENS(5,short)_)
I will try this as well to see what happens.

Thanks for the responses, i do appreciate the help.

Peter

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