I do use SH3Commander. Be aware there is a special version required to use for WAC, and a special way of installing and running it.
Even so, I do occasionally experience the random CTD when using Commander. I just had one three days ago, when starting the fifth patrol with my current Kaleun. I'd updated my patrol logs and crew lists for the forth patrol with SH3Commander, then started SH3 using SH3Commander, then awarded promotions, medals and qualifications in-game before starting the 5th patrol . . . and CTD.
Eight times.
I started SH3 using SH3Commander only the first time, and for the next 7 started using Sh3.exe. So the ninth time once I started SH3 I backed up the load game selection to the "after mission in base" (not sure of the exact wording) from the forth patrol, re-awarded promotions, medals, etc., then started the 5th patrol again . . .
Voila!
So SH3Commander (even using the special version for WAC) did something that SH3/WAC did not like. What that is, I have no clue.
I do know that WAC seems to act funny with Commander. For instance, if I select the GWX 8 hour fatigue model, when the game starts my crew experiences fatigue. If, however, I then save and load, they
stop getting fatigued. I have no idea what else might be effected. For instance, I also have "Malfunctions & Sabotage" selected; I have no way of verifying if any malfunctions or sabotage effects are cleared if I save and reload. The same with randomized crush depth . . . which I have
no intention of discovering my U-boat's crush depth!
So, no, you aren't the only one experiencing this. I don't think anyone, at this point in time, as any real clue what is causing the CTD when using SH3Commander.