Updating the thread just in case any one else has this problem (stated in the OP). This isn't likely since it seems to have something to do with LSH3 5.0, but here's a brief summary of what I found.
It appears that there was some sort of conflict between the file group 'Turm7c_5_hd.xxx' and how ever the game places emblems on the turm.
To find this out, I moved all of the Turm7c_x files and started the game. With this modification the appropriate emblem was visible in game. I then added back in each file group Turm7c_1x then started the game. Emblem still visible, then 7c_2, etc. Up until I added back in Turm7c_5_hd.x. When I did this the emblem dissapeared again. Removing '5' and adding in '6, 7, and, 8' also yielded a configuration where the emblem was visible.
So, something is going on with one of the Turm7c_5 files that is keeping the emblems from showing up in LSH3 5.0 (and 5.1, no new Turm files are installed with 5.1).
I know that Turm7c_5_hd.x is the turm for a /41 controlled by AI. Because of this, I'm not sure what would happen if one of those boats happened by while the appropriate turm files were missing. Might a crash potential.
It is possible that the issue was caused by something that I tweaked somewhere along the line. When I uninstalled LSH3 5.0 (back to vanilla) I got consistent CTD at the initial start up screen. I did the re-install dance (Thank you
BL!TZKR!EG and
THEBERBSTER for the guides, big help), and on a fresh install, the emblems showed up normally. So, it could be a conflict within LSH3 5.0 or something I did.
In any case, I figured with a fresh install, I'd give LSH3 2015 + H.Sie's mods a try and see if I could get my existing career (that started in 2014 with 5.1) to work with them.
Turns out it wasn't too hard. Had to do a little bit of a dance to make it work. The indexes for the flotillas are changed so I had to tweak the numbers in the career and career_0 files, but then every thing seemed fine. The emblems are showing up normally as well.
-Cheers,
z