Weird COUNT(*) results in MySQL 4.0.16

After upgrading our OS X 10.2.8 Server, the Drupal sites we are running exhibited hilarious read counts. After someone on the Drupal site confirmed COUNT(*) was behaving properly on his 10.3.2 server, I decided to perform a clean install of our server, which I just finished.

To verify if the COUNT problem was gone, I tried a couple of queries against the standard mysql database.

SELECT COUNT(*) FROM user;

results in

COUNT(*)
6

But

SELECT select_priv, COUNT(*) FROM user GROUP BY select_priv;

returns

select_priv   COUNT(*)
N             144115188075855872
Y             288230376151711744

The incredible count is still there. It should be N = 3, Y = 3.
Anyone else who experiences this problem? Any suggestion for a solution?