This sounds like you have a smoothing group splitting a uv island. Set your smoothing groups by your uv islands with a script, triangulate and then rebake. Without pictures I can only guess as to what the problem is.
I'm new to this texture baking and creating thing, but i know some of the basic stuff but what i don't understand is why i need to triangulate the object? the low poly one right? And after triangulate the object, do i need to uvw unwrap it again ? i will post later a screenshot, but it is a simple cube, no smoothing…