For the Benchmades I've owned with this problem, I had success with this method: loosen all the screws (complete disassembly isn't necessary, and with screws that small, why tempt fate?) and see how the blade falls between the liners. Use hand pressure to hold the knife together in a manner that causes the blade to center itself between the liners. Sometimes this involves pushing one liner/scale assembly "up" relative to the opposite liner/scale set. Still holding everything together with hand pressure, tighten the screws down, but be careful because you can pretty easily strip the threads on the backspacer screws. When you're done, you should have a knife that's better aligned than before. I have to mention, however, that newer Benchmades tend to be less sensitive to this sort of work - the components drop into place no matter how you screw with the component alignments. Then again, I haven't seen a newer Benchmade that needed this sort of adjustment.
PS - make sure that the blade itself isn't crooked. Take it out and sandwich it between two pieces of plate glass or something similar. You'll have to remove the thumbstuds, of course.