Just a suggestion but did you set the start date for SH3 Cmdr and the game to the right year?

Yes. I selected successively 1942 and 1943 from SH3 commander, but when I arrive in SH3 and create the new campaign, 12th Flotilla (based in Bordeaux from 10/42 to 8/44 and using type IX) is never available. By the way, only the standard game flotillas seem to be available...

May I suggest you PM Beery or JScones; they may be able to help and at the very least look into the matter.

Sorry I cannot be more helpful.

Thanks for the suggestion, will do !

12th and 33rd Flotillas aren't starting flotillas, so you can't start a career in these flotillas. The option exists in SH3 Commander only for setting up a single mission or for manually setting up a career in progress where the career has already progressed to a time when 12th or 33rd flotillas have been made available to the player.

I guess we should make a note of this in the readme file.

Do you mean you can transfer to these flotillas once they're available or do you have to manually modify the save games to be effectively transferred ?

You can transfer to these flotillas - but that's already part of the game. SH3 Commander doesn't alter that. All SH3 Commander does in terms of flotillas is make it possible for the game to have more realistic features based on the flotilla you're in. Currently there is no SH3 Commander content for 12th or 33rd flotillas, so choosing the listing in SH3 Commander won't do anything at all. If you set SH3 Commander to 12th Flotilla or 33rd Flotilla it will use the standard game's flotilla settings.

I hope this helps. SH3 Commander may be a bit difficult to figure out at first. It's not like a regular mod. Instead of directly altering the game in a solid and lasting way, the changes that SH3 Commander makes alter the game in very subtle ways (especially in terms of the flotilla-based changes) to give a more realism-focused play experience. For example, in the regular game every flotilla you join has the exact same start date for a Type VII, but with SH3 Commander it's possible for all flotillas to have their historical start dates for the Type VII and for every U-boat type. This change won't be noticed by many people, but for folks like me who like things to be as realistic as possible it is nice. The date-based and submarine-based changes are more apparent to the casual gamer than the flotilla-based changes.

How exactly does this work? If I set up a career in 1939 and choose, say, the XXI in the 1st Flotilla nothing in the menu screen tells me that this is historically incorrect.

If you choose those options, you will still not be able to use a Type XXI in career mode because the game will not allow you to use a Type XXI in a career. All it will do is configure the game so that your choice of an XXI in single mission mode will work properly - i.e. you might get a 1st Flotilla emblem on your Type XXI boat. Currently, nothing has been adjusted for the XXI, so you wouldn't see any difference in a single mission anyway, but the potential exists. One thing that has been addressed is the crush depth of the Type VIIC/41 - so if, for example, you take out a Type VIIC/41 you will get a different crush depth than the standard Type VIIC. This is not possible with the regular game, because both U-boats use the same file to determine crush depth, but with SH3Commander enabled you can take the Type VIIC/41 deeper than the Type VIIC. Try using SH3 Commander to set up a test mission with a VIIC and take it beyond its crush depth, then restart the game with settings for a Type VIIC/41, do the same crush depth test and see the difference. You should find that you will get deeper with the Type VIIC/41 than you can get with the Type VIIC. This is not possible without SH3 Commander.