Marlin, I had the same issue when I replaced my rotors, brake pads, and brake lines. I figure with all that work the pedal should be solid as a rock, but I could step on the pedal and the VX would stop, but if I kept pushing on the pedal it would eventually go to the floor. The VX never moved during this little exercise, even on a decline. After repeated bleedings, and replacement of a hardline or two that I thought was leaking, I finally decided that it was the master cylinder. I made the mistake of letting the entire system run dry, and sit open, for a day during the rotor/pad replacement process so that may have caused my master cylinder seals to crap out, or maybe they where on their way out anyway.
Anyway, I replaced the master cylinder before Moab this year, and it seems to have solved the problem. In truth the pedal still feels softer than I would have expected, but it doesn't hit the floor any more.
"The major difference between a thing that might go wrong and a thing that cannot possibly go wrong is that when a thing that cannot possibly go wrong goes wrong, it usually turns out to be impossible to get at or repair."
-Douglas Adams, Mostly Harmless