Well, just to cover all bases I have reviewed the SH3Cmdr changes in R2.4. The only change that *may* affect the game is that now the correct U-boat availability dates is a selectable option, *OFF* by default, whereby with previous versions it was *ON* by default. I doubt that's the problem (otherwise lots of other users would have commented), but you may want to ensure the option is checked and try again. All other changes were just to the SH3Cmdr interface and don't even affect SH3 itself. From what I've read so far I'd be surprised if your problem is related to SH3Cmdr or SH3Gen. Have you recently installed any other mods at all?
What happens if you try with an earlier patrol (copy your campaign first or you'll lose the later patrols)? If you can reload an earlier save game and play through and all is OK, then it's perhaps something quirky with that other one patrol, perhaps as GE suggested, maybe it's a corrupt save file that is "carried through". I wouldn't even try to guess - I'd cut my losses and replay it from scratch.
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