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This is the second time Hammer has done this, even on two different machines. It seems like it has a limited number of compilings, then it decides that what ever I changed wasn't important and only displays in the game last time. It still, however, likes to take forever to compile, like it's trying to trick me.
For instance, I was tweaking my lighting on my map, and the light was on one side of the map. I compiled it, it looked sucky, I move the light right in the middle, and it still had the same angle as before.