I've seen AmiDock get confused with some prefs before (can't remember what though, maybe a prog I added). Try renaming envarc:sys/amidock.prefs to amidock.prefs.back or something then rebooting.
It might come up with an error saying it can't find the prefs after the reboot, if it does then it's a problem with the prefs file and not AmiDock. Either start from scratch or copy the prefs file from the CD.
If that doesn't work try copying AmiDock from the OS3.9 cd back into WBStartup.
