2012 Toyota Matrix 213,000 kms (132,000 miles) AT 1.8L

Brake pedal has recently become soft.  When engine is off, pressure builds and brake pedal holds firm.  When engine is on, but car is in park I can push the brake pedal to the floor. 

Brake pedal is easy to push when car is driving, but it sinks down more than it used to.  The car still stops, but takes longer at higher speeds. There are no warnings lights on.

 I do not see any external brake fluid leaks and brake fluid reservoir is full.  I changed all pads and rotors and bled the brakes 2 years ago, but no recent work has been done on the braking system. 

I bled all 4 calipers yesterday, but the problem still persists.  I do not hear any hissing noises or strange sounds coming from the braking system.

I’m wondering if I have bad master cylinder or if air became trapped in the ABS module.  Since this just become a problem and the hydraulics were not touched in 2 years and I don’t have any ABS codes, I doubt I have air in the ABS module, but how can I rule this out?

If the brake master cylinder has gone bad, what would have caused this?  I’m diligent with my vehicle maintenance and keeping the brake fluid clean.  I didn’t think brake master cylinders were known to fail on Toyota’s.  Did I do something to damage it or did the o-rings just give out?

If I need to replace the brake master cylinder is it ok to get a new one (not a reman) from my local Napa or do I need to order a new one from Toyota?

Many thanks for the assistance and guidance.