Yes you always need to wait around 12 hours for things to stabilize. Racks are odd creatures it is always an average often the temps are never exactly what you want every where, often it is finding an acceptable range.
IR guns are fantastic tools but need to be coupled with understanding of how they work and the limitations. They do not measure plastics well, translucent shiny objects reflect IR and this is what they measure. The rate of reflection is higher than what they are calibrated for (think brown paper) and the corresponding reading can be off quite off even. I would suggest adding a bit of paper to the back as a target to measure and then remove it when you are happy. Simple and easy and removes the possible emmisifity errors and bounce errors.
What stat do you have? If I recall it is a herpstat? or am I mistaken. Herpstat, helix, ecozone, herpkeeper all have highly accurate spec'd probes they can be used to check other thermometers. Some stats learn how fast or slow a heater responds and adjusts the power curve to match. I have noticed with a newer set up and a relatively high or low powered heater it sometimes when you adjust it takes longer to stabilize as well. When it has been operating for some time in wide variety of situations it is faster. I believe this is related to the power curve still being learned.
Where you place the probe may also help regulate the rack as well. Most use the middle shelf and often the top is a bit over and the bottom under. Of course the room plays a major part in the regulation the more stable the better and often the closer to correct ambients the better. There is a reason why most larger breeders keep racks in warm humid spaces.
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