Recognition of the existence of this problem snuck up on me slowly. I don't remember whether the light dawned while I was watching Trading Spaces or a design program on HGTV, but one day, I saw it two or three times in very short succession and it finally registered on a conscious level.
Damn, I said to myself. Why is the hardware misaligned on all these peoples' cabinets? (By "hardware", I mean the door pulls and/or knobs, the things you grasp with your fingers to open the doors and drawers.) I started to watch for it. Sure enough, show after show, there it was: Sometimes the hardware on a pair of doors was slightly offset vertically, and occasionally horizontally as well. Careful inspection showed that drawer hardware was also sometimes slightly off, though this was much harder to detect.
Though I'm not hung up on symmetry, that offset looked awful and the seeming epidemic piqued my curiosity. I sought further evidence of it, and to be quite honest that focus pushed the question of "why does this happen?" out of my head for a while. What can I say, I'm easily distracted. Once the "why?" occurred to me, though, I found I already knew the answer. Here's what is going on:
Pre-assembled cabinets arrive with their doors and drawer heads attached, though they are usually attached quite loosely, as an intentional time-saving courtesy to the installer. The cabinet manufacturer knows that before installing the cabinet boxes, a competent installer will remove all the doors and drawers, and possibly part of the hinge as well. Doors and drawers are removed for at least two reasons:
To protect your shiny new doors and drawers from incidental damage, and To protect the installer from being beaten about the head and shoulders, or knees and groin, by flapping doors and sliding drawers while they are working with the cabinet.
Once the cabinets are installed, the doors are reattached and the drawers are slid back into the cabinet. Then the doors and drawer heads need to be adjusted. Most modern cabinet doors attach to the cabinet box with six-way hinges. These hinges allows the door to be nudged slightly in a variety of directions — up, down, left, right, in, and out — until everything lines up properly.
If the drawer head is separate from the drawer box, it should be adjustable up, down and sideways. (If it's part of the box itself, you are S.O.L..) Tightening the drawer glide screws may reduce binding, and some fancy glides can raise or lower the drawer as well.
Only after all the tweaking is done should you carefully mark the doors and drawer heads and drill them for the hardware.
All these people with misaligned hardware probably had an installer who fell victim to the temptation to drill the doors and drawer heads after they had been detached from the cabinets. Unfortunately, the necessary hinge and drawer head adjustments put these good intentions to shame.
Once the door and drawer head drillings have been screwed up, the only thing you can do to fix them (short of refacing or filling the holes and painting) is to buy backplates for your hardware, and hope and pray that the backplates can cover the old holes when you re-drill everything. A backplate is just that: a small decorative metal plate, usually roughly oval in shape, that lies on the face of the cabinet door or drawer head and serves as a backer to the hardware.
Research has taught me that some artisanal cabinet makers (as opposed to large corporations) may adjust the hinges at the shop. This situation is beyond the scope of this writeup.
Supplemental causes for hardware misalignment include:
Poor cabinet installation. The cabinet itself was not installed level and square, and needs to be shimmed. Wear and tear. Over time, screws can loosen slightly and cause a door or drawer head to slip. This may be helped along by abuse, e.g. repeatedly slamming a door or drawer shut, or hanging one's weight on them. The door has warped. People very frequently mistake poor hinge adjustment for door warping, but once in a long while, the door really is warped.
References
Personal experience.
A rather spirited discussion amongst cabinet makers which includes debate on whether to hang the doors in the shop. At least one reference (slightly below the diagram of an end panel) is made to putting the pulls on after the doors are hung.
http://www.woodweb.com/knowledge_base/Hanging_Cabinet_Doors.html | 
