Commodore had a year on them and couldn't get it right
Birdie was made by Trond Werner Hansen, a norwegian Amiga user. Not by Commodore. It's an unofficial hack to make the WB nicer. It does a lot of things that it shouldn't... :-)
The reason for Startup-Sequence, User-Startup and WBStartup is that some programs are supposed to run before LoadWB. Programs like Birdie which hacks the way windows are drawn.
User-Startup is pretty safe to toy around with, Startup-Sequence is lower level, still pretty safe if you take the appropriate precautions, but still - warranty void if you toy with it :-)
Now, take a deep breathe, read up on the manual to birdie and other patches you might have running. Birdie is a strange bird which isn't too happy if you crowd it.
