Hello davemachews;
What you are describing is normal computer behavior and nothing to worry about.
When your computer first boots up, have you noticed how the BIOS searches for all the drives connected? The Bios does this in its own designed order: Primary IDE, Master - Slave, Secondary IDE, Master - Slave. Newer computer have added SATA 0, 1, 2, 3, 4 or even more. And if you are not using any IDE drives and turn off the resources to the IDE controller, then the BIOS skips that and starts with the SATA Drives. The point is the BIOS assigns drive letters based on what physical channel the drive is plugged into.
Windows has its own rules on what drive letters to assign. You can even tell Windows what letter you want assigned to a drive.
Checkdisk is a program that loads and runs before Windows can start so it does not know (or care) what drive letters are assigned by Windows. It goes by how the BIOS searches and finds the drives. This is normal and nothing to worry about.
Cheers!
Robert