Because it's a complicated process, apparently. (I can only refer to Changwattana in Bangkok, though...)
Person 1 hands out numbers, if you're early, and you have to line up far from the entrance. Then, when they open, everyone hurries to the doors, where one has to line up again, while person 2 calls out/checks numbers. Going inside, one has to line up again to have docs checked, and given a number. After 90 to 120 minutes of waiting, number gets called, again documents get thoroughly checked, and also up to 10min. pass while the IO checks the documents, and updates everything in the computer. One gets a new number, and asked to wait outside, usually 30 to 60min. - Passport and docs pass through several hands, checked and re-checked over and over, before being ready to get stamped by, dunno, person number 15? - Highly effective process, which Immigration in Jomtien surely has to follow too...