We have a small claims case against a former landlord over the deposit.

Per their attorney they have agreed to settle the claim, and a mutual release in exchange for the settlement check.

The defendant has not yet signed it, is this the normal order of things and is there anything we should watch out for?

Should we require the check to be in certified funds or something? Or should they have signed it first?

If I understand you correctly, you're suing the landlord.  If that's the case, then basically they give you a check (according to your settlement negotiations) and then you sign the release.  The only reason I see to have the landlord sign the release before you do is if he's made claims against you as well.

they threaten to at one point to try and get us to drop it, then after our response agreed to settle for returning deposit and filing costs rather then defend against statuatory double damages, so we want the release as well,

(maine is weird in that they allow attorneys and attorneys fees in small claims) and there is some odd case law in relation to deposits from what I could find