Heart rate zone

A couple days ago I was reading Matt Fitzgerald's blog, he had a great post about heart rate. After reading it I did some verification with my latest workouts. As an example on Sunday I was running a ladder, for the first 30 minutes of it I had to stay in zone 1. According to the data that I gathered with my Garmin 305 I ran at a pace of 6:11 for that first 30 minutes. I had a really hard time to stay in zone 1 during those 30 minutes, I remember my watch beeping a lot to tell me I just hit the beginning of zone 2. Overall for those 30 minutes my heart rate average was 143 and my max heart rate was 150. Now this morning I went out for a 45 minutes run, it was supposed to be an easy run so I just went by feeling. I ran at a speed where I was feeling really good, usually something between end of zone 1 beginning of zone 2. Then I analyzed the data a little bit and I was surprised to see that on the same path as Sunday's run my heart rate versus pace were really different. Today I ran at a pace of 5:46 and I never hit zone 2 during the entire workout. My average heart rate was 136 and my max heart rate was 146. I am not really sure how I can explain this, the main difference between those two workouts were the time of the day. Sunday's was during the afternoon and today's was early morning. I also had an Aquathlon on Saturday which could explain it, at least a part of it. Does that mean that we can't really rely on heart rate data when we train, or that we can't only use this. How can I run at a pace 25 seconds faster with a heart rate average 7 beats lower? I guess that will have to try to train more by rate and less by heart rate zone, or at least use both to make sure I always get the maximum of every workout.