You have to talk to the Mole (and later, the Platypunk) in the first room of the arena (near the blue and red chests). I had beaten Captain Crow and his crew 3 times prior to beating the game, and I never found him again until I heard that you've gotta talk to these monsters to find him again.
For me, the mole first mentioned Captain Crow, I left and came back immediately and he congratulated me for beating him and gave me some prize. Left and came back again and the platypunk was there I believe, mentioned CC again.. and THEN I was able to fight him again.
4th fight - He sends a Marquis de Leon against you. 5th fight - Last fight with the captain, win and he joins you.
Don't forget to talk to the mole again after and he'll give you another reward.
Edit: Captain Crow appears at random whenever you enter a zone that is under adverse weather effects. Just keep going to the map screen and entering blinking zones until he shows up. --- "I miss seeing Mario decapitate Sonic or Sonic peeing in Peaches *******. there's just no soul nowadays." - ShiNoBinn