Your batting assignments for the #1 pitchers could be the culprit. Try going into the roster.dat file and modifying all of the SP1 pitchers' batting assignments for vs. the NL.
What you do is open it in WordPad. It looks something like this:
000000017,0 00b87d5f5,1 0fff0da1f,2 SP1,3 -1,4 SP1,5 9,6 SP1,7 -1,8 SP1,9 9,;
What happens is that sometimes people move the #1 pitcher out of the slot instead of putting someone there or simply clearing the rotation, it assigns a (-1) as if it is for an AL batting order.
You correct this while in WordPad; select the "replace" command and input SP1,5 -1. Replace it with SP1,5 9. Simply do the same for the SP1,9 slot. Make sure all of your commas and spaces are the same.