The only cases where I have seen this behaviour is when Windows does not recognise that the hardware has already been plugged in once and assigns a new letter. This could happen if another USB port is used or the firmware of the external storage unit was updated since the last time. Or when a controller is acting as a middleman between the OS and the disks.
Are the disks directly presented to the operating system (since you say it is JBOD) or does some black magic occur in the enclosure holding the disks? In the latter case, this could be a hardware specific issue. Having a look at support options provided by the manufacturer might help.
In any case, a workaround exists for sync applications which work independently from drive letters: instead of indicating a path with drive letters, use the serial number of the disk or the disk label, which do not change every time the volume is mounted. Such sync applications include SyncBack or FreeFileSync but I am sure many more applications support this as well.
Cheers,
Fabien