I didnīt have that problem with TWoS from version 2.0 - now 2.2.3. When you sight or detect a convoy, save the game and reload. Before start the approach. If you are playing for 3 hours, detect a convoy and continue to play, could cause some problem. But I didnīt have they in my installation.
Steam version? I have DVD version.
Memory of your GC?
My SH5 TWoS runs at 60 or more FPS; I limited the FPS with Nvidia Inspector to 35 FPS. And donīt play in window mode and/or synchronization.
Good luck and good hunt!
Fitzcarraldo