sonofbruce: i found your post and have a similar issue. i have two widely different counts and its not due to posts deleted. i am running WP 2.7 | akismet 2.2.3.
my dashboard says that akismet has spam-ssassinated 957 comment spams. however the akismet stats page on my site gives my correct counts of 69,###.
this issue first manifest itself after installing WP on a new server and populating the mysql database with a previously exported table backup. of course, there have been a few WP and akismet upgrades since then but i believe the reinstall as the issue.
for reference, the akismet counter also shows the lower number and not the more correct higher number.
of course, no one likes spam but if i'm going to keep track of things i'd like a consistent reading.
does anyone have insight into which two data sets akismet is querying so i can rewrite things or otherwise realign my stats?