I had a similar experience when arriving at T1 in May, but like pwalhx says, it’s the same everywhere. I'm airline ground staff at Leeds Bradford and it is extremely frustrating when dealing with inbound flights as passengers just want to leave as soon as possible, but there is always a queue. I was surprised and slightly pleased when I saw the queue at Manchester in May as I thought it was just poor organisation at Leeds.
We have had several feedback sessions at Leeds from some of the ground staff to out managers/airport company managers and as the situation at Manchester has proved, when dealing with the UK Border Agency, there is naff all anyone can do about it. It reflects very badly on the airport operator but at the end of the day if it was up to any airport the queue would be non-existent. The UKBA seem to do what they want, when they want. On a personal level at Leeds (and I’m sure at Manchester) they seem to have all the desks manned at the times when only one or two flights are being processed at the same time, but when it comes to peak passenger flow the border staff seem to go somewhere (!!) I do however think that the general arrival procedure at Manchester is fairly good, I have never not had a queue but because of the expanse of the terminal the queue is constantly moving.