Sounds like you need more Ice & Water Shield. My parents had a similar problem- we ripped off the shingles and put I&W up the entire slop (around 12′), just to be safe. Haven’t had a problem since (12 years).
As a note, typically you want the I&W up at least 3′ past the wall of the house. If you’ve got deep overhangs, the 3′ of I&W that you have isn’t enough.