When you set up your iPhone with a Google Apps account, it’s best to set it up as an Exchange account and NOT a gmail account as Google tells you in the set up. For whatever reason, they don’t tell you this in the account settings page. Here’s the link on how to properly set it up to sync to a I-phone
Setting it up as a gmail account may work, and in fact has for me on several occasions, but every once in a while, it just doesn’t work.
This is what Google says right from the link in the Forwarding and POP/IMAP link:
Why do you suppose it’s different?