I've seen something similar.
In my case I have three Rosewill RSV-SATA-Cage-34 hot swap bays which support 4 HDD each. They are natively configured as 1 through 4 but I wanted to set them up as 1 through 12 (rather then 1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4) which took some doing to arrange correctly. I tested the configuration by swapping in and out a 2TB HDD which worked as expected with respect to drive number detection and physical position.
However, one time, far removed and unrelated to the earlier test, I swapped in a HDD and it wasn't numbered correctly. Tried it again in another slot and it was more of the same. After a reboot it all went back to functioning correctly.