I boil on my kitchen gas stove, no propane burner. The volume boiled off is always a lot less than what Beersmith says, so I don't think that that would be the problem.
Yesterday I came home very late, and decided to drink one of my homebrews, Denny's rye IPA actually. I usually pour my beers in a Duvel-like tulip glass, but this time I took a Hoegaarden hexagonal glass. I also was careful to leave the bottom 1 cm in the bottle, and, lo and behold, the color of the beer was much lighter.
The lees I can understand, but the glass? Or does my beer look different from bottle to bottle? Or am I crazy?