Ok new problem...
I installed SH3 Commander and attempted a new Mediterrainean campaign with the S-100 type, I deleted the faulty intro video and checked the "skip intro movies" option on SH3 Cmdr. This time, when the main loading screen appears, the game would load about half way and bam, CTD. I disabled all the mods using JSGME and attempted to try GWX alone without any mods but same thing still happens, CTD every time the loading bar would reach halfway. I also checked the "rollback automatically after exiting SH3 function".
Earlier, I tried the S-boot mod in the Med without SH3 Cmdr and everything worked beautifully, I just wanted to use the beautiful med colours you get with the program. Something must be conflicting between the mod and SH3 Cmdr...
This is really frustating...