For those who have wished for Chatter to pass alerts to the alert manager whilst you are in Chatter (mailbox view), Marc says it will be in the next beta release. Iím pretty sure I have seen posts regarding this. I like to use Butler for all alerts. Chatter has its own LED and repeating alerts but it seemed Butler and Chatter would compete for control. Chatter would always pass alerts to the alert manager (so Butler could use them) while you are not in Chatter if the option was set to do so in Chatter's prefs. But now it will send them either way.

A big thanks to Marc.