I experienced this very same issue. I was able to track down the problem to a conflict with Runway 12 library objects. As it turns out, the objects for 4 of the 6 ships in the task force have the same name (GUID) as assigned to several jetway objects from the Runway 12 library, and your simulator is drawing the jetway objects from the Runway 12 library instead.
I was able to fix this by decompiling the bgl files and assigning new IDs to the 4 conflicting ships. I checked my new IDs versus the entire Runway 12 object library and the default FS2004 objects, and thankfully I have no conflicts now.
I recompiled the new bgl files and voila! All 6 ships in the task force now appear properly. The issue with the St Louis scenery would also be resolved since your scenery will not try to accidentally call upon the USS Hornet or some of the escorts in place of the jetways :-)
If there is anybody with this problem that is still using this scenery with FS2004, feel free to reach out to me for the corrected files. If there is enough interest I can contact the authors to try to obtain authorization to release a patch to repair this issue.
