Mike, the first point is that you've double-checked that the coaxial cable from the sub out on the Blu-ray player is actually plugged into the correct LFE input on your 645. Then, make sure the cable isn't defective by switching in another cable from a channel that you're sure is working.
To test whether the sub is actually working with the Blu-ray, keep all the settings the same but disconnect all the speaker wires and see if you hear sub output when playing something that's bass-heavy. As Dan suggests, it's curious if you were getting actual sub output with program material but not with the test tone.
