TM pro reef is an alkalinity of 7 at 1.025. I like what JDA advised, even though I think stratification is a thing of the past unless the salt has been very...very well travelled. It's much more likely your alkalinity test is incorrect or your salinity test is incorrect and frankly I'd do a second test of each and recalibrate before claiming a salt is the problem. I'm not saying it's impossible, the TM issue was not related to alkalinity or salinity, and the batches are large.
Instruments fall out of calibration faster than your average salt will stratify so if you haven't recalibrated your measurement tools, I would look at those first honestly.
Check your reagent dates, check your refractometer, check that your pipette and your cuvettes are well cleaned and free of smudges, and if you're using a digital refractometer, make sure it's accurately taking the temperature of your water, otherwise your salinity will measure lower.
For what it's worth, depending on the test you used, it could just be reading the test incorrectly or taking the test sample past the correct equivalency point.