Thanks Dave, strangely enough - both the flights I have done back to Heathrow after having these problems have gone perfectly, with no problems at all.
When you say 'Back to Heathrow' do you mean with Heathrow as your destination airport? I'm not at all sure this is the issue but you can give it a try. Click the SIDs/STARs button and type EGLL in the box, then press Enter. If the value 'Minimum FAF Alt' at lower right is not zero, set it at zero and try the departure from Heathrow again and see if there is any difference.
Yes, the 2 flights I have done with Heathrow as the destination have both been fine.. It's just the departures from Heathrow that seem to have the problem.
The minimum FAF was set for Heathrow to 2500, I shall reduce it to zero and try another flight tomorrow.