To clarify (because your version of events, as written makes my head hurt)..
You failed to notify the DVLA of change of keeper when you sold your car. This was your legal obligation.
The garage said that they would take care of that by requesting a new V5C by sending a completed V62 form.
The car was sold the following month.
At some later and as yet unspecified date it was caught speeding.
A NIP incorporating a requirement under s. 172 was sent at some later date to your "last known address" and deemed served 2 working days later.
You did not respond to this requirement, due to being unaware of it.
An SJPN was issued for the offence of failing to name the driver, and presumably also for the underlying speeding offence. You did not receive this as it was sent to your previous address (your last known address).
You were convicted in your absence of the s. 172 offence (MS90 is the DVLA endorsement code). You would not have been convicted of the speeding offence as there was no evidence that you were the driver.
You got the conviction set aside under s. 14 Magistrates Courts Act 1980 as you were unaware of the proceedings.
You are now facing the s. 172 charge again, the difference being that you are now aware of that.
N.B. The timeline, such that it is, is based on your account, and may well not be accurate.
At first blush, this is your own fault for failing to notify the DVLA of change of keeper. There is a statutory defence to failing to name the driver where it was not reasonably practicable to provide the information required - however, simply being unaware of the notice is not in and of itself sufficient, reasonable practicability will include the wider question of whether or not it would have been reasonably practicable to ensure that any such notices were brought to your attention, such as by complying with your legal obligation to notify the DVLA of change of keeper.
However, all might not be lost. Or it might.
Ordinarily, when a vehicle is sold to a trader, it is recorded as being "in trade", until such time as it is sold and registered in the name of the new buyer.
Off the top of my head, the V62 process can be quite lengthy as the DVLA are supposed to write to the registered keeper to give them an opportunity to object to the transfer.
What we do not know is whether the V62 process was still in progress at the material time (when the car was caught speeding, or when the police looked up the RK details) - in which case everything is your fault, or whether it had been completed and was showing as "in trade" and you were sent the NIP as "previous keeper" - in which case it would seem that your prior failure to notify the DVLA would have made no difference and the defence would seem to have legs.
When was the vehicle sold to the dealer?
When did the dealer sell the vehicle?
When did the dealer receive the new V5C?
When and how did the dealer register the vehicle to the buyer?
When was the vehicle caught speeding?
When was the NIP/s. 172 sent to your previous address (we could work this out from the s. 172 offence date)?