Regarding the false positive issues: I have been reading the logs for smtp qmail current for the past couple of months. I wanted to keep an eye on the RBL performance. In Ray Mitchell's post he notes that one RBL was generating a number of false positives. I concur with his opinion and have striken that particular list from my group, as he suggested. In reviewing my logs, I am sure that will cure darn near most of my false positive issues. Overall I am very pleased with the performance of the RBL technique. I have not found a reason to implement SpamAssassin. I am running a Bayes filter on the Outlook Client (Mozilla comes with one...)to pick up the ones that get through.
For your second issue, the vanishing email: Bit of a stumper. The smtp qmail current log shows all the email being received by the system and in turn how it is dispatched (accepted or rejected). If nothing is showing up relative to a particular piece of mail from a particular route I would conclude it is not being delivered.
Though you can telnet to the SME box from your workstation/client, is the route open from the email SMTP source? Being unfamilar with your network particulars, I can't offer much of an opinion. But would suggest that as an avenue of investigation.
There may be firewall / router restrictions along the way blocking delivery.
I doubt this helps much.