Your altitude, potentially cold weather (dry air) and large surface area probably did it. You can also boil off more by having your burner at 100% full throttle all the time. The boil should be hard, but it doesn't need to be crazy.
Also- do you transfer trub into your fermentors? I do but get crazy amounts of cold break (around a gallon) so that affects my final volume. If you're leaving that behind, you also need to adjust your preboil volume. You probably just didn't start out with as much as you needed.
I can't be arsed to keep up this list of what's in the fermenters, but hey, check out the cool brewery I'm opening up!
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