Yeah, those bubbles can be tricky. Make sure your master cylinder cap is on tight during the process. If it's loose, air gets sucked back in and ruins your bleed.
That point about air getting sucked back in is huge. But don't forget, air can get trapped way down in the system too, not just at the master cylinder. On my old truck, I had to gently tap the brake lines and the calipers with a wrench while my friend pumped the pedal. Tiny bubbles were hiding in the curves of the lines and the abs unit. Sometimes you have to annoy the air out of all the little spots it likes to hide.
That tapping method sounds like a real hassle. Do you work from the master cylinder down to the calipers, or just hit every low spot you can find? For the ABS unit, does tapping usually get it done, or do you need to run the pump with a scanner too? Using a regular wrench seems like it could damage the lines if you're not careful.