Check the Options for Facebook app and check BlacBerry Message Application and in the bottom of the options try choosing Leave email notification messages on mail server...
The email address you get your facebook notification on must be setup to receive on your BB if I am not mistaken. Is it?
Posted from my CrackBerry at wapforums.crackberry.com
I think that's the case.
It stopped working on mine twice, one time because I changed my email address on Facebook and forgot to set that email on my Bold. I think, instead of being delivered to the mailbox, the messages go to the application.