Ok, this sounds crazy but lots of lots of experience with the threaded stop nut style cables has showed me something I don't really understand.
Align the swivel exactly like the manufacturers instructions indicate. Now, do your adjusting at the cable end, not the swivel.
This.
What you are dealing with is the point of reference. The point of reference being the coarse cable mounting adjustment. I have removed a transmission and just unbolted the cable mount bracket from the pan bolts. Did my transmission servicing, installed the same transmission in the same place and had this issue. There might be just enough slop in the mount holes to cause this issue to happen. Hope this helps.
Digger73 (Mike)
