Have you look at this link:
Are you using Juniper branded optics? If not, you need to get at least one and test with that. Is auto-neg enabled? You can not set the speed (see the link), but duplex on EX4600 should be Full always.
Maybe output of show chassis hardware,show interface terse and show chassis interface extensive would help. For the last two you could do this for one or two of the interafces.