Auto verses manual shifting firmness

When I let it shift on it's own in the drive (third) position it shifts fast and firmly but if I shift manually from 1-2 or 2-3 it flashes even though it is at the same rpm as when shifting automatically. I am aware that it uses a band instead of the sprag when manually shifting 1-2 but don't know if that would effect 2-3 shifts. I have searched but no match. This is a used transmission untouched other than a new filter and fluid. Appreciate any and and all help.