I had a similar issue myself recently with my street bike on the front. While I agree it could be the cup on your master, usually if you listen close you can here it suck air.
Here are two tricks I picked up from a Honda wrench I know that fixed mine despite putting over a bottle and a half of fluid thru it with no results.
1) Ziptye or otherwise keep your brake on overnight. This way, any bubbles in the system can move up to the cylinder. While doing this it also helps to tap known problem areas for air bubble (banjo bolts, cylinder base, etc) with a plastic mallet. I emphazize tap, don't take your frustration out here.
2) If step one didn't work, try removing the entire assemble and then hang vertically overnight with cyclen up and caliper down, tapping here helps once again. With a straight shot it seems to move bubbles thru the system better.
One other thought, are you sure your bleeder is closing and seating properly?
Good luck, I know how incredibly frustrating that can be.