you used to be able to bank cheques same day for clearing if you paid a tenner, though that was a few years back, dont know if they still do it, but when you wnt to be sure it isnt gonna be cancelled....
If you have the terms or contract of your agreement you should be set. They have no way of defaulting because you have legal proof that they owe you! Stay on them untill you get what you deserve. Good luck!
I'm very pleased to hear that you got it sorted in the end.
I know that some people can find that asking for money can be very uncomfortable, but as you found in your case, sometimes just a friendly call can get results.
The fact that the original cheque was unpaid by the bank probably explains why they were so slow in sending it to you. They probably didn't have the funds available at that time.
As a side note : Even if you don't have clear terms and conditions of sale there is a legal default of 30 days for business to business transactions. If the invoice is not paid within that time you are legally allowed to charge interest on the debt too.