Had the issue a few times as well (though not ex UK), taxes related to mileage upgrade I did online and the system failed to flag and collect online (so the first time I was not even aware there was an extra charge). Each time they collected, once at the check-in when I passed by there, and the other times when I had checked in online it was at the time of boarding.

Thanks Wtravel and ET for your comments... thought I saved my self some cash, but oh well!!