Even though the gsx.cfg for the aircraft had the proper values, it was going to left side.
Then either that GSX.CFG you were looking at wasn't the one used by GSX, or it didn't had the proper values. The airplane editor will tell you which GSX.CFG is used, either the one in the main airplane folder, or the one in %APPDATA%, with the one in %APPDATA% taking the precedence.
When I went into aircraft editor and did 3d customization, it had the position in center of aircraft as if it was at the zero cg
That's the default position for an airplane were the fuel position has never configured (or for an airplane that was not configured at all).
also appears gsx default is to go to left wing.. it does not go to fuel port location, but parks off the wingtip. It is always the small fuel truck.
The small truck doesn't "always" appear. It appears when the refuel point under the wing is too low for the larger truck, that is lower than 3.40 meters. If the larger truck cannot fit under the wing, the smaller one will come, on the side specified by the refuel point (left if negative, right if positive), provided a refuel point IS set.