Just flushing the system will never get all of the old (dirty) fluid out of the master cylinder. The fluid becomes dirty because of deteriorating rubber components in the system. This will also cause a soft pedal due to brake fluid going around the seals in the master cylinder.
Try replacing the master cylinder (remember to bench bleed the new one) then flush the brake system again, then go do a few ABS stops and recheck the fluid, if it looks all clean you should be OK, if it is dirty again flush it again. You may also need to flush the clutch master/slave as well.
I had a similar problem with the fluid always looking dirty and that is what I did. Hasn't been dirty lookin since.
