ahhh, that may be the infamous save game bug which has been haunting SH3 and SH4 skippers for years and ruined way more careers than enemy ASW ever did. Everyone has their own ritual and no one has found the magic formula. Based on other recommandations, I save on the nav map, surfaced, game paused, well away from enemy ships, spin three times, scratch my dog's belly and hope for the best...
save early and save often, YMMV.