Strictly speaking, it's not a problem with renaming per se', but an occasional issue that stems from it.
Once on my computer, and once on my mates, I have renamed subs using the Roster/Ships/American/etc etc method. This, for some inexplicable reason, leads to the game either only allowing me to start my Career in Pearl Harbor in 1941 (despite selecting the Asiatic Fleet), or it gives out the same mission constantly (My mate has Reconnoitered Yokohama 5 times and counting

)
Is this constant same missions thing present in unmodded copies, or is it inexplicably linked to renaming ships?
Any input is welcome. Thanks lads.