I have a similar problem suddenly with wp-shortstat (which I am addicted to, it's a great plugin 'til I broke it). I've searched the forums, seeing if I missed anything.
Problem: wp-ShortStat stopped counting. It says 0 hits for several days (should average 200+). Shortstat was working previously for weeks. It might've stopped when I upgraded to WP1.5.2 but that might not be the cause.
I went to myPHP-admin and deleted the 2 wp-ss tables from the database, re-activated the plugin.... it rebuilt the tables it needs, but still not counting hits.
I don't recall, and can't find any documentation saying, that I would need to place a certain code in my Header (as I needed to for Counterize and other plugins), so if I have forgotten that and potentially deleted it, please remind me the trigger code?