Crash after upgrading sub?

[THEBERBSTER]

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without the Commander Mod

SH3Commander is not a mod but an application.
By your response you are obviously not using it so is not relevant to your problem.

Windows 10 is not compatible with SH3 so it needs to run in compatibility mode for Windows 7.
Crashes loading saved games is a compatibility issue.
If your game is installed in the Program Files (x86) directory you are likely to have problems as this is a restricted directory and does not like alterations being made to your game especially mods in JSGME.
Applications like GWX and SH3.exe should be run as administrators.
On your first patrol you should not upgrade your boat.
Check your documents folder and make sure you can see the SH3 save game folder.
Check that your gpu is setup correctly.
Post #239 Changing The Nvidia GPU Settings
Peter