[Crannogman]

It is odd, maybe I can check the rsrdc files later tonight. IRL, the Asiatic Fleet had 3 sub tenders at Cavite in Manila Bay when war broke out. 2 of them were hastily evacuated and well on their way to Balikpapan when big Jap air raid came on Dec 10; the other tender was moved to Mariveles and there continued to service boats until it was scuttled at the fall of Bataan in March. The shore installations at Cavite continued operations until Christmas Day '41. By that time, most of the fleet had re-based to Surabaya, although the sub tenders continued on to Darwin for January and Tjilatjap for February before retiring to Fremantle by March 1.

So you should make for Surabaya if Manila is no longer an option. I hope to be able to release my Atolls & Allies mod soon, which will (among other things) make the bases and tenders more realistic.