Hi there,
I myself am with the Halifax and have experienced the evil that is their 'reasonable' bank charges. I also had the opportunity to gain some inside info on these matters.
Handy tips - It only costs the banks est. £5 to return a DD, also to stop a cheque free of charge tell them you believe it to be stolen they can't charge for prevention of fraud or theft.
Q.1-A: Did you called the bank to pre-warn them of your error in your calculations?, as this isn't clear.
As a loyal customer with an existing overdraft they could have offered to increase the overdraft for 1 month to cover the cheque so you didn't get the 'over agreed limit' charges of £39 + interest & or cancelled the cheque for the lesser charge so you could inform the recipient and re-issue the cheque when the funds were available.
As for loan protection it's all in the wording of the policy - if it specifically says in the agreement that your circumstances will be covered then they should come to some arrangement. Try asking to be put through to the branch you hold your account/loan with.
I hope this helps.