I have observed this problem as well in my PBEM game. Every base in Malaya is assigned to the Burma HQ despite the fact that all bases were captured by LCU's assigned to the Southern Army command. That includes Singapore, which was captured when the SA command was one hex away, in Johore Baru. What is even more frustrating is the fact that I cannot reassign any of the bases to the SA command, and yes, I have LCU's in the hex that are assigned to the SA, including that HQ itself .
I'm wondering if the fact that I transported the SA hq by ship to Malaya has anything to do with the problem. Also, the 3d Air Division hq was tranported to Khota Baru fairly early. It is assigned to the Burma hq, but it did not participate in the capture of any bases, and I switched it to the SA hq before Singapore fell, so I am really confused about that one.
Little help, anyone?