According to several (1) (2) (3) threads, the offical Gamecube US servers are experiencing technical difficulties. Apparently when you connect and press A past the Minhiro information, the ship select bugs out and sends you to a random ship. After you materialize, you get disconnected and have several windows open (like the ship select still on the screen). Also, it will apparently freeze your game if you wait too long to disconnect. Item loss has been reported.

Hippie recommends that you either soft reset, pull the ethernet/modem cord out, or open/close the lid to force the game to save. As a reminder, you can soft reset by holding B + X + Start. This will save your game and return you to the title screen.

We will keep you updated on this story! In the meantime, you can use our forums to post about this issue in this thread.

EDIT: Seems this problem has stopped for the time being.
EDIT 2: Seems the problem is back again. We advise you to take extra precautions before going online, just to be safe until ST solves this problem. And as a reminder, do NOT shut the gamecube off if this happens. Do a soft reset instead of shutting the Gamecube off.