There's a lot of layers that need to be peeled back in order to determine a definitive cause-and-effect. A few things that come to mind would be the type of melatonin yoi are taking. Sublingual instant absorption, time released -sustained release or dual spectrum –instant mixed with sustained release? Timing matters with all of the above. If you are taking any of the sustained release, ideally you should take this 3-4 hours before bedtime. For sublingual, I would suggest at least an hour before your scheduled bedtime.
The idea of taking it up to several hours before your scheduled bedtime is to mimic your natural pulsatile secretion of endogenous melatonin. Taking it right at bedtime forces a phase shift on your gene clocks (BMAL1/CLOCK) that creates a mismatch between your brain and your peripheral tissues.
Another area that could be a potential reason is your specific microsomal isoenzyme– CYP1A2 gene variant. If you're a slow metabolizer of this particular isoenzyme, or if you consumed any caffeine several hours before bedtime, this can inhibit the clearance rate of melatonin. They both, caffeine and melatonin are metabolized by CYP1A2. Your endogenous estradiol levels can muddy melatonin secretion and clearance rate. In either case, if may be. If you're a slow metabolizer or competitive inhibition by caffeine or estradiol, this will keep that melatonin you took lingering around longer than it should. In which could give reasons why you're waking up groggy.
If you find time, cross reference every supplement and pharmaceuticals you're taking and see if there's competitive inhibition to CYP1A2.
Then there's this fancy little p-glycoprotein that interacts with melatonin. To put it simply, p-glycoprotein works in several different facets intracellularly. One of it's primary functions is to move (efflux) molecules out of a cell. Melatonin acts as an inhibitor of p-glycoprotein. If by chance you're taking some other pharmaceuticals or nutraceuticals that are sedatives that rely on p-glycoprotein clearance, melatonin just put the brakes on its clearance rate.
On a final note. There have been some melatonin manufacturers that inadvertently, either intentionally or improperly synthesized serotonin and sold it as melatonin. This will definitely screw your sleep patterns up. I highly recommend buying USP verified melatonin.
