Virgin Atlantic Flying Club - Connecting at LHR when arriving on different tkt

After a lot of lobbying, my firm has added VS to it's list of approved carriers and we have a corporate fare to NY. However, I regularly travel in Scandinavia and last week wanted to go STO-LHR-EWR. My agent said the SAS and VS tickets had to be seperated as she could not include a Virgin leg at our corporate fare. Consequently, the check in at STO said they were unable to check me in for the vS leg as it was a seperate ticket. Thinking I could check in at the gate or lounge at LHR, I went merrily on my way, only to discover that the ONLY place you can check in for VS at LHR is the landside check in. So I rushed through immigration etc and got to check in just after the flight closed. Luckily the later flight was full in J so they reopened the flight to get me on, however, this only happened because it was convenient to them!

So, question: can anyone see a way around this happening again? Is there another check in option I have missed? I have just booked my next US trip on BA to avoid this hassle...