This is very strange, @windyknollgoldens. What camera are you using? I have seen similar issues on Nikon cameras when Auto ISO is turned on in an obscure menu, making it appear that the ISO is being set manually, but when the shutter is released it just uses whatever ISO the camera thinks is best.
I have worked with lots of cameras too and have not seen the exact issue you have described before, so I want to hope that it’s a setting (or combination of settings) somewhere and not an actual defect with your camera.