EDIT: Problem solved, solution is at the bottomHotSake wrote: Did you test it with a new Mammoth or one that already existed before you made your changes? You need to spawn an entirely new ship to see the changes.
Ok, so I tried creating a new Mammoth, no joy. I then went and edited just the Titan scene file and removed all the docking mod stuff and started a new game. Still no joy, the Mammoth still has 5 bays and accepts a TS and the Titan has 2 bays.
Changes made to the SRM cat files, and re imported, are these:
M2_Titan_P_Scene.bod : Deleted BDS Mod entries at bottom
TL_Mammoth_P_Scene.bod: Deleted from *.cat file
TL_Mammoth_P.bod: Deleted from *.cat file
dummies.txt: Reverted top docking entries to vanilla
--SOLUTION--
I extracted the entire mod contents, and noticed there is not only a Mammoth_Scene and Titan_Scene, but there is also an Argon_M2_Scene and Argon_TL_Scene. I deleted the BDS entries from those scene files, and now everything is working just fine. After work I plan on writing a little script that will go through and delete the DBS entires, since they have been nicely commented.
Looks like I'll have my perfect MOD after all. I know I'm a bit obsessive on this, and I do miss TS->TL docking from X2, but I think the bombers on ships stuck on the ship surface are just goofy.