Whilst I don't work for HMRC I do have a lot of experience in working with them (and I'm not a beancounter) but maybe you wish to consider the fact that it is not the individuals that they are looking at but the company as a whole. BA have - as we all know - had issues recently which may have raised their risk profile within Government. As there is a framework of paying these allowances so that they do not attract Tax or NI (see
http://www.hmrc.gov.uk/manuals/eimanual/EIM05250.htm if you really want to) then it could be a double check that what is being claimed is as it should be.
However, I would like to point out that this doesn't mean that BA is under any specific investigation - it could just be that it is their turn to be fully audited