Sad to see that some pilots never see anything beyond a piece of concrete or tarmac and the ATC voice at an airport. At large airports (certainly in the UK) ATC are just contractors and are bound by the rules and demands of the airport operator. In my experience, although a controller may know that a runway slot has been allocated, he or she doesn't give it much thought when an aircraft is ready to go or to land - the important thing is to shift the traffic in the most overall efficient way. I'd be surprised if there weren't a lot of controllers who were as surprised as the pilots at the apparently cavalier attitude of BAA.
If you've got a letter like this, take a look who wrote it and go speak to them - I'd lay money it wasn't ATC.
PS - and don't blame ATC for recording the take off or landing time either - it's got to be done for lots of reasons but that's probably where the slot allocators get their data.