That is indeed strange... you have the needles and glass on some of the gauges, but not the actual gauge, then you have one notepad, but not the other, and no NavMap on the desk, so it's the "linked" things that are messed-up. Did you delete the Save folder?
If you would, de-activate the mod with JSGME. Empty the Save folder. Re-activate the mod with JSGME (don't forget that Patch), and check the LAA activation on SH4.exe again, then start a new career and see what your boat has in the Control Room... Be sure that you have the Windows display set to the Native ("Recommended") setting in the Windows Display Settings. Have SH4 set to the same thing in it Graphic Settings dialog.