Bayes not working after upgrade to 4.50.14

[chardlist]

I successfully upgrade to 4.50.14 tonight, I love the new features
especially the hires time reports.

I've noticed that after the upgrade MailScanner (or spamassassin) is no
longer paying attention to my spam.assassin.prefs.conf file.  The bayes
database is not being used in the path I've specified, and other options
I've configured in there, such as bumping the bayes score, 

I'm on a cPanel server so I upgraded using a scripted provided by
www.waytotheweb.com which has been successful for me in the past and was
adapted for MS 4.50.14  That's about the only unique thing I can think of
that might make my upgrade a little different.

My before upgrading my MailScanner.conf file had this value in it:

SpamAssassin Prefs File = %etc-dir%/spam.assassin.prefs.conf

The after the upgrade that directive is not present.

MS 4.50.14
RH 9
Exim 4.52

Thanks for any help!

-Brendan