What do you mean when you say that they "cleared the cheque a few days later"?
If I have a doubt about a cheque, I give it to my bank and they send it for "special clearance". That means that the bank on which the cheque is drawn gives the ok. It is the equivalent of walking into the branch on which the cheque is drawn and asking them to give you cash in exchange.
Normally, you just lodge a cheque. The banks give you credit for it on the assumption that it is valid. If it turns out to be a dud, they just debit it from your account.
Brendan