I put all my crate tokens together before reading that they should be kept separate from the rest. Was there anything special about the crate tokens in Daedalus that would effect the game if you had all the tokens mixed?

Yes, and no, there was a printing error in Novgorod, that could allow cheating, but I really don't think it's very likely. This is a pretty common question and there have been threads on it before.

One solution is this: miah000.blogspot.com/2011/06/tannhauser-crate-markers.html

Miah999 said:

And what an awesome solution this is^ Nobikaigan made some for our copy. They're a good fix and they're awesome looking =)