The positive bit is you did pay, and the amount paid covered your parking before you actually paid. The negative is that no payment had been made when the CEO happened along. So submit some informal representations on the following lines: -
Dear Sirs
Re PCN <PCN Number> dated <dd/mm/yyyy> served at <hh:mm> at Felixtowe Road Car Park
I wish to submit representations against the above PCN on the basis that when I arrived to park at Felixtowe Road, I was not aware that the time period for payment to park had been extended from 8am to 6pm to a 24x7 requirement to pay and display. The ticket machine was out-of-order, so with a train to catch I decided to catch the train and pay by phone. Unfortunately I was only able to make payment some time after the PCN had been served, but as there is only a single payment of £2.50 covering any time after 6pm, I paid the full fee required, as there is no other option.
Whilst I accept that your CEO was correct in issuing the PCN, I would ask you to note that full payment of the parking charge was made, albeit after the PCN had been issued. In view of the circumstances I have described, I therefore please request that you use your discretion to cancel the PCN as the council did receive full payment of the parking charge. May I also state that now I am aware of the new charging hours, I will now pay on arrival at the car park.
Yours faithfully