Cheeky blighters!
Having spoken to the Virgin Flying Club help line this afternoon, it would seem that if you redeem air-miles for an upgrade for part of the journey then any air miles earned as part of the journey are not calculated or added to your account.
What does this mean? Well, we paid cash for economy tickets from London to Havana, and Jamaica to London and used air-miles to upgrade both legs to Premium Economy. We expected to get air miles for the 'real' cash paid element but it seems because we redeemed air-miles for part of the 'experience' the system discounts any air miles earned even though you are entitled to them.
I rang them up this afternoon and had this explained to me after noting that neither Mrs yt or me had been credited with any air-miles for our two journeys (?). To be fair to Virgin they knew exactly what had happened and manually entered the information to our accounts. Every little helps and all that.