if this isn't a particularly helpful answer ... but the thing is, I've often wondered whether the Passport Office works in cahoots with the Post Office Checking Service. (Y'know, preferential treatment given to those prepared to fork out the few quid extra ... ... being that BOTH are Government-controlled outfits = in turn, more funding for the Treasury.)
Here's hoping this wholly unsatisfactory business can get sorted out soon for you, Sean - and for all the other long~suffering applicants into the bargain.