The difficulty in sinking the ships is indeed based on Grew Wolves or NYGM, both of those mods make things more difficult.
The "behind the desk" thing you got was the "Simulate a realistic career length" option, where after so many patrols you're sent to train new recruits or work a desk job. You can simply click on your Status and get back into active duty. Or leave the realistic career length option unchecked and patrol till you die.
If you pick "return to duty" you should keep your same boat and crew.