When Pro Tools 1st boots up it doesn't see 003 and automatically goes to Aggregate.
Thats fine. Let it go to the aggregate,
Just quit protools and make sure the aggregate device contains your 003 first.
You on a mac?
Is the 003 recognised by your operating system? Can you play music from it? media player/itunes/whatever?
Is the firewire port known to work?
Try a different one, especially if you're using a front port.
Are you using any firewire adapters? 4pin to 6 pin? anything like that?
Could you do a factory reset of the 003 incase there's something funky going on?
I think there's a utilities button or something like that and you follow the onscreen instructions (on the digi).
Can you try a different firewire cable?
Just to clear up any confusion, you've definitely installed the latest 003 drivers for the correct operating system and PT version?
Check that, It's easy to get wrong.
I think they do standalone drivers and some other kind. Sorry I can't remember but it's worth a look and a read.
And the big one. Have you trashed all Pro Tools preferences?
I know you've uninstalled and reinstalled, but i'm not certain that everything's trashed that way.
Again, idk what OS you're on, but there's a very handly preference trashing tool for osx.
Here it is.