Is there a way to fix it so chinook does drop crates? As it is right now I'm spawning the crates on my server myself. Do I have to restart my server or? This has had me frustrated for a while now

This turned out to be a server glitch at the time and it was eventually patched. Crates should drop normally these days.

If you are using a skip nights plugin, usually they reset the time on the same day, so the time keeps skipping backwards which prevents various events from triggering, so this is probably your issue.