it seems to be a common, but not definate occurance.
A friend of mine has the exact same problem, which proved very confusing when i sent him a .vmf we were co-making.
I'd just added some displacements, and he IM'd me asking why i'd put the grass on the wrong side. Compiled; it looked like it did in my hammer, but in his hammer it was the wrong way round.
So i have no real answer, but simply the info that you're not the only one.