Calbeck you were notified all along that Manila had fallen, you just missed it. Pay attention to your incoming msgs, it is important, trust me!!!!
I sailed out of Cavite on Dec 9 and, reading my msgs, got a msg that the Phillipines had fallen and my new base was Surabaya. So I knew where to go, knew how to manage my fuel.
When Surabaya fell during my 3rd patrol I was reassigned to Fremantle. All I had to do to know this was
watch my msgs!!! Or if I forgot, just scroll back thru them until I found it.
Assuming that something is crapped with your install, and you're not getting these msgs to start with, there is a thread here somewhere telling you where to look in your save game files to find your currently-assigned base.
Good hunting
DH