Do you know what causes that "MSGID_FROM_MTA_SHORT" flag to be set? It's adding a whopping 3.3 hits to my legitimate emails sent from a PHP app (a thank you for your order message).
According to http://au2.spamassassin.org/tests.html it was added because "Message-Id was added by a relay"... but what the heck does that mean? Is that because the mail server is named server1.MYHOSTINGCOMPANY.net?
If so, do you know any way to make it send these through the mail.MYSHAREDHOSTINGCUSTOMERSNAME.com server (which is just an alias for the same server)?
I believe you can either, change the struture of the email. or set a lower score in the spam assassin rule.
I have no problem sending to a local account from php, with Spam Assassin. I did get that error once when I had the email generate all the data in 1 straight line. Are you adding any headers to the mail via PHP ?