OK update. Just went out and pumped the pedal and it responded as though nothing ever happened, very firm first press. Started the engine and the same, no issue at all. Could this be an intermittent problem where as the module may be on the way out? I wonder. None the less I will be flushing/bleeding the system ASAP.
Ok, this is good info. Intermittent issues can be difficult to diagnose. Now, a common scenario for having no brake, then when it pumps up after a few pedal or lever actuations it acts normal is that the pads are being pushed out when the wheels are turning. You brake, it pushes the piston/pads back in, but takes a couple presses to get braking action, so first one is "oh sh*t" with nothing, then maybe you get a little the second and finally full normal braking the third press.
The three most common issues where the pads get pushed out are:
Axle spacer in the wrong position. (or binding tension arm on the rear caliper. Bolted to the side of the tab instead of centered on the tab)
Warped or damaged brake rotor, (you should be able to spin the wheel and see this.)
Bad wheel bearing allowing the wheel to move around. This is harder to visually see, but removing the wheel and spinning the bearing with your fingers should tell you if it's smooth or rough/notchy.
Put the bike on the center stand and spin the rear wheel by hand. Smooth or rough? Can you see any waver or in and out of the brake rotor when looked at strait on from behind? After spinning, does the brake pedal have less firm feel? And if you grab the wheel and try to wiggle it side to side, does it move? (this often won't happen unless the wheel bearing is really bad)