I agree with AlfaJack, it is most likely air stuck in system. I found this with my '94 Civic. Haynes manual says that ABS systems should not be bled by home mechanic, but I ignored that. It just seems to take a little while. The fluid can come through without bubbles, then suddenly when you think you're done, a bubble will appear.
Need to make sure you keep bleeding the system until fresh, clean fluid appears at the bleed screw. If fluid seems to be rid of bubbles, but stilll looks dirty, keep bleeding. This is because brake fluid absorbs moisture over time (don;t mean to teach you to suck eggs), therefore making it compress when the pedal is pushed.
A note on drilled discs - they can increase pad wear, obviously due to the edges of the holes acting like a grater! Don't drill then to solve a problem that shouldn't be there on standard brakes.
I'm off to plaster my skinned knuckles after doing a cam belt change on my Honda Civic!
Ant