Boy, was Alan right... Don't use the version of MySQL (4.0.16) that comes prepackaged in MacOSX 10.3 Server. Man, does it stink.
Update to 4.0.17, using the handy dandy installer provided on MySQL.com/downloads - it works great, and even starts on boot (unlike the version that comes with panther...) Just bit the bullet and updated versions on careo.ucalgary.ca, and the weird database behaviour has apparently disappeared.