I used RB's Flag & Pennants mod without any problems.
Try disabling any extra mods that change the u-boat .dat files. If the emblems return, pick the one you want, sail a patrol, then re-enable the extra mods after you've saved and exited your game.
This might work because I already had my sub emblem before I used RB's F&P and LRT.
Hope it works for you.