I'm guessing when you disable relative extrusion distances, S3D puts a M82 at the top of the file telling the machine to switch to absolute extrusion distances. When you have the "G1 E30.0 F500" command, I think you intend to use relative distances. So you could just update the script to say this:
M83 ; switch to relative extrusion distances
G1 E30.0 F500 ; prime extruder
M82 ; switch back to absolute extrusion distances
Or just zero the extrusion distance before and after the prime. Then it will work in both absolute or relative mode.
G92 E0 ; zero extrusion distance
G1 E30.0 F500 ; prime extruder
G92 E0 ; reset extrusion distance again