Woh guys! Let's be clear here. SH3Cmdr does NOT have anything to do with the actual colour of the water. The colour you all refer to is NOT part of SH3Cmdr, but part of the underlying mod, in this case NYGM.
All SH3Cmdr does is force SH3 to use the *existing* Med water textures when undertaking 29 Flotilla careers (it also forces Arctic water textures when in 11 Flotilla).
Thus the real solution is to fix (if indeed it is a problem - that's not my call) the water textures that are part of NYGM (contained in EnvColors_Med.dat). Then everything will be peachy.
However, if this is not possible, you can very easily remove the remapping from SH3Cmdr by doing no more than deleting ..\SH3 Commander\Flotilla\907\data\Env\Env.cfg. You'll see it is merely a text file.
You'll then get Atlantic water textures back, which IMHO is not realistic either. Thus, perhaps someone should have a go at fixing the Med texture in NYGM, or trying ones from other mod packages (or even the one from stock SH3 itself).
Also, don't forget that you should adjust SH3Cmdr's "Water clarity" setting when in 29 Flotilla. From the SH3Cmdr help file: "When undertaking careers in 29 Flotilla it is recommended that you disable the 'Adjust water density' option, or initially change the setting to 8 and adjust *up* from there to your liking. This is to cater for the lighter Mediterranean water textures. "
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