It beats the hell out of me why things work one place and not in another.
It's mostly my best guess by just looking at the files involved.
You can also open the dats in S3D and see textures not rendering properly.
Here's my suspect list and that's just 1.3 files.
NBB_Bismark\NBB_Bismark.dat
NBB_Nelson\NBB_Nelson.dat
NBB_Queen_Elisabeth\NBB_Queen_Elisabeth.dat
NBB_Revenge\NBB_Revenge.dat
NBC_Repulse\NBC_Repulse.dat
NCA_Deutschland\NCA_Deutschland.dat
NCA_Lutzow\NCA_Lutzow.dat
NCA_P26b\NCA_P26b.dat
NCVW\NCVW.dat
NCV_Illustrious\NCV_Illustrious.dat
NDD_1936A\NDD_1936A.dat
NDD_A&B\NDD_A&B.dat
NDD_C&D\NDD_C&D.dat
NDD_SU1\NDD_SU1.dat
NDD_Type7y\NDD_Type7y.dat
NECT_Hansa\NECT_Hansa.dat
NKGHAN\NKGHAN.dat
NKGHAP\NKGHAP.dat
NKLCS_Nagara\NKLCS_Nagara.dat
NLUS_Bremen\NLUS_Bremen.dat
NOM_Paula\NOL_British.dat
NOTM_T2\NOTM_T2.dat
NPPE_\NPPE_.dat
NPPQ_\NPPQ_.dat
NTUS_\NTUS_.dat
T07B\T07B.dat