I think this has a lot to do with how you've phrased it to them, no offence intended. If you'd simply put down that you had your licence since the day you passed your test, but you had X conviction on Y date with Z ban length then this wouldn't even be an issue. I'm guessing you've incorrectly stated that your licence has been withdrawn or taken back or however you phrased it by the DVLA, when actually it hasn't at all. They may physically have asked for the card back back, and they may physically give you a new card, but that doesn't mean it's a new licence.
Again, if I get nicked for speeding I have to send my photocard off to be endorsed. That doesn't mean I don't have a licence in the mean time and cannot drive, nor does it mean that it's a new licence when it comes back.
You really need to speak to them again and be VERY clear in your terminology. No more saying that the DVLA have taken your licence off you, and more saying that you've simply had a ban of Z length for X conviction. It really is as simple as that, I really do think you've massively over-complicated this and confused people that you've spoken to.