Need urgent advice on stamp duty penalty

Me and my partner bought our house in November 2007. We were FTB ers and not all that clued up. My solicitor at the time told me that we hadn't registered for stamp duty in time - we paid it all but didn't send off some form. Solicitor said she'd dealt with it and I thought nothing more of it.
2 years later and we are selling our house and at the exchange stage. Whilst looking through my partner's paperwork - I find an unopened letter from Revenue & Customs dated Feb 2008 saying that we were late in paying our Stamp duty and now have a penalty. I paid it online immediately and also told my current solicitor - she says she can't proceed with exchange until she has proof from Revenue & Customs that its been resolved. They say that when have received my payment they will fax my solicitor.

I'm really stressed as I don't know if/how this could mess up sale of my house. Can anyone offer me any advice or experience?

That all sounds in order to me, it was an unfortunate oversight on your part it would seem. Hope it all goes through for you now.

Thanks for that - but what I'm worried about is whether not paying the penalty (until now) means that I'm not legally registered as the owner

It sounds like OP is in the UK and this site is Irish (we don't have a Revenue & Customs department in our government)

Yes. it seems so, as FTB's here aren't liable to pay stamp duty, & the OP states that they did.