I solved the problem. It turns out that the SATA gets lined up first in the drive list (sda, etc.) on that motherboard when it is used, and the MB is first when no adapter card is used.
This was confusing, but once I realized it, I needed a solution to specify a specific drive, no matter what the drive was called in a given boot.
So I had to specify the drive I wanted to boot off of which might be sda with no adapter and sde with the adapter. Using a UUID specification allowed a consistent reference to the disk that I wanted to boot off of.
My original post is not exactly accurate as to what was happening, however others have had similar problems and emailed me on other sites, and indicated that the UUID specification worked for them. So I understand that the question is disjoint from the answer, but I have addressed this in the interest of helping others similarly situated.