I continue to get email from readers complaining that the Chooser persists in erroneously assigning their serial printer to the modem port, even though they have previously selected the printer port for it. Here is Apple's explanation for the most common cause of this (taken from an Apple Discussion Board item):
This is caused by AppleTalk. AppleTalk tends to take over the printer port when active, and this will prevent a serial printer from using it. This prevention makes the serial printer's driver choose the modem port to print to. The act of making AppleTalk inactive (either in the Chooser or the AppleTalk control panel) is not sufficient, since the resources loaded at startup. The best way to make sure it stays off is to make it inactive, then immediately shutdown. When you start back up, check the Chooser to make sure it stayed off. However, be aware that using file sharing or Apple Remote Access will make AppleTalk active again. In this case, a better workaround is to make sure the Apple Remote Access Client is installed, this grants a new option in the AppleTalk control panel. This new option is called "Remote Only", and choosing it will then route AppleTalk to that, freeing up your printer port for use by your serial printer.