Patch attatched below, modified from this mailing list post http://groups.google.com/groups?selm=aomivb%2416bu%241%40FreeBSD.csie.NCTU.edu.tw&output=gplain modified to apply against snort-1.9.1, snort is now rock solid for me.
Created attachment 9868 [details, diff] Patch to get snort working on Alpha
Thanks for the patch! This should now be fixed in snort-1.9.1-r1.