graydon, I agree with you totally on the "other factors". I've been able to learn a little bit more about some of these things more recently.
Wind seems to make a bigger difference than I had previously thought. I keep track of the weather in my log (from a local weather station on
Welcome to Weather Underground : Weather Underground). Interestingly, 5 of my top 7 commutes have been when there's no wind at all. This even though only 16% of the days have no wind. Also, previously I'd only paid attention to component of the wind that in my direction of travel (head wind or tail wind). Based on my data, I now see that the cross wind component actually correlates more highly with FE.
Also, like you said, sometimes you just catch the lights wrong. What I've begin to notice, as well is that it can make a big difference WHICH lights you catch badly. I think bad things that happen early (before things warm up) have a more negative impact than they would if they were near the end.
Also, I've begin to notice that my focus can make a big difference. Sometimes if I'm not paying attention and really focusing, I can do quite a few things to hurt my FE without realy noticing--like not really looking ahead for the lights and trying to catch them right.