Andy,
I am sure you have probably tried this, but as we have not seen this problem before, is there any other addons that you may have installed recently? Did it happen at EGLL both times? (Maybe you could look for a newer AFCAD file for Heathrow) Is it with the same plane both times?
Basically I guess we need to eliminate whatever we can from the problem solving process so if you could try a flight from different airports with different planes and see if the same situation occurs. The only other problem I can think of is look at your FSUIPC version, make sure it is up to date, also are you running software along side the flight logger that may interfere, possibly FSP or something although I have never heard of a module or addon that uses FSUIPC cause this sort of problem.
Good luck, keep us posted.