It really is a shame that in the year of all the updates they did from 2007 to 2008, that they never fixed some important oversights, such as the radar antenna shaft versus the conning towers, the "New Command" versus the "Re-Fit" - which is a new conning tower, the early "New Command", nor the clothing of the sailors, such that they don rain gear when it's raining and not waiting until gale force winds and rain going sideways come, but also the winter clothing that does not show up when you are in the arctic circle. Ask for a weather report, and they do not tell you the temperature nor the barometric pressure - what kind of report is that?... lol
Anyway, we still do experiments with the "upgrade" process in the game and will continue to do so, hoping to find some little thing that can help in this issue. As an example, I've tried to edit the Save files to "roll-back", with nothing but failure thus far, but it seemed to be close the last time where I did make it into the office with a different sub, but failed when I went to go on patrol. If we can at least get that to a working point, we'd have a work-around... Again, in my opinion, I think it should fail outright as soon as something is not right, but since you were close to a proper date, it did OK for a time.
As a little addendum, perhaps if you just go back a little, prior to the transfer to Majuro, and just run from Midway only, that maybe it will do better?... I dunno. I have not tried that yet myself, and you may end up with the same thing there, and have wasted your time... But the Balao stays at Midway for the duration, and does not get transferred by the game to Guam, the way Majuro does, which might be where the trouble with going there is triggered. I dunno.
