This is happening to me as well, but only when i try to merge 2 different images to create a merging effect. I do this to try and simulate displacements. Everything looks perfectly matched in photoshop, however when in hammer goldsource or in-game (CS 1.6), i get:
(sorry about low quality, temp. textures)
It's basically 4 images in there; the upper-right one tiles horizontally & vertically; the upper-left tiles vertically; the lower-right one tiles horizontally; the lower-left does not tile, but like i said before, i don't get those seams in photoshop.
I've read a while ago, in an entirely different game engine forum, that this may be an issue related to some calculations in Open GL...However, i don't remember exactly what it was about, neither did i fully understood the topic. The math in there made my head explode.
Oh, this happens both on brushes made at an angle or linear.