A little update on the ship thing:
I can't find the solution for the ship problem, though I was able to replicate the problem. I've compared the code for the map files that manage ship upgrades in RPGMaker and the only thing I did was change the names of the ships from Japanese. I've even started a clean/new save and used the original Japanese commonevents file, and the bug persists.
However, I did manage to narrow it down - looks like the problem is the Caraval ship. If you upgrade that particular ship for either upgrade, it'll permanently prevent you from upgrading any future ship with the upgrade you selected for the Caraval. On the bright side, it's ONLY limited to the Caraval, so if you upgrade any other ship with either upgrade, you won't encounter this problem.
My advice is to avoid upgrading the Caraval at all and move on to a better ship. I'll continue to check the variables in the game files as I'm seeing a complicated mess here and it's gonna take some digging before I can figure out what's going on.