The Dir state will depend on your drives, some dont really care but some need it to be either Hi or Lo, not sure about the Geckos as its been a long time (7yrs) since I set them up in the Bridgeport.
It going in the right direction at the moment has no bearing on whether you have it set right or not as there are other factors that can control which direction the motor moves, these are obviously the Dir state, the Reverse setting in Homing and Limits and lastly the motor wiring itself. The two that can be used for Dir change, if it is wrong, are the latter two and the former should be kept at the manufactures recommended setting. Obviously changing the wiring is not so easy as choosing the Reverse setting in the software so the reverse setting is the usual one that is used.
The Dir Prechange setting could also be your problem as if its not set high enough for your drives then it may be missed until the next step by the drive so again could lead to accuracy issues. I always had my Geckos set to zero for both pulse width and dir but it all depends on the computer you have. Zero is obviously not zero and the actual time will depend on the latency of your computer, so setting zero on one computer may be the equivalent of setting 2 on another with less latency.
Hood