I wouldn't worry about adding mods then, I was just curious if maybe you had added one, and it was affecting your game. The game has what some refer to as "layers", where one set of files runs from December of 1941 to March 1942. A second set will then load and run from March 1942 through to September 1942, when the next files takes over. Sometimes, if you're in the "between" time, where one file finishes, and the next loads, there will be no traffic for several days.
You might also be sitting in a bad spot for the traffic, especially for a Manila boat, which wouldn't have surface search radar, so you have to rely upon your watch crew, which when you're submerged, are probably in the aft torpedo room playing cards and gambling away their next pay... You need to be on the surface and moving at All Ahead Standard (usually), do a patrolling search pattern, so that you increase your chances of actually "seeing" something. You could experiment sometime, where you spot a distant vessel, lock it the periscope before you dive so you can identify it. Then dive to periscope depth, and it will disappear. Say you spot it at 9200 yards, and when you go to periscope depth, you may not see it until 5200. That's how much of the ocean surface you're missing by being below at PD. You might have air search radar, and if you do, pay attention to it. Watch
for some pointers. Your screens may not be exactly like his, but the technique is sound, and allows you to actually "hunt"... Silent HUNTer, remember?...
Even if you don't have air search radar, it's better to be up top so you can see. Just be ready to hit the "Crash Dive" button anytime something is spotted...