I'm familiar with similar issues Josh
Our set up - '08 MacBook Pro, FW400 to Pro40, FW800 to external drive, USB hub feeding an Edirol UM-1, an Alesis Trigger I/O & DMXIS Hardware box
Firing up the MBP with everything hooked up rarely results in everything actually connecting properly first time. However, carrying out the following procedure works for us
every time:
1 - Make sure Pro40 is turned off
2 - Make sure any USB plugs are disconnected
3 - Fire up the MBP
4 - 'Remove' USB devices from within the Audio/MIDI window (that's actually set to 'Open at Start Up' on our system)
5 - Turn on the Pro40 and wait for it to connect
6 - Plug in the USB stuff and you're away
I've often wondered why there appears to be a conflict and how it's fussy about a connection order (or even how I came to discover a consistent work around!) but once it's up and running, there's no further problems so it's kinda second nature now
However, if you don't have any USB devices, then I've no idea what your particular issue might be