The grid set through SH3Cmdr is more than just for the player's benefit. When set while docked at your
own base, it is recognised by the game just like any SH3-generated grid. Useful for WaW players and others that just don't like what they've been given.
The problem is when you dock at a "friendly" base. Put simply, docking at a friendly base "breaks" SH3's relationship modelling, thus resulting in NULL grids as no appropriate value (ie link) is found.
This disconnect goes beyond the patrol grid itself, hence why attempting to correct with SH3Cmdr in these circumstances has no effect.
Fortunately, there are three ways around this problem:
1. Always complete your objectives *before* docking. Thus, you will not lose renown (remember, it's not really until you return to your home base that you have completed a patrol. SH3 just doesn't recognise this aspect, hence why every docking is considered a patrol completion).
2. Start the patrol, save and exit and use Stiebler's SH3Patrol to correct. Then restart the patrol again.
3. Start the patrol, save and exit and manually edit the newly-created .psc file located in your career's savegame folder - the value you need to change is fairly self-evident.
(only follow this one if you know what you are doing). Then restart the patrol again.
Personally, I follow #1 (least hassle for me). And as I am currently in the Indian Ocean and hence have already compensated my renown values (see a previous post of mine in another thread), I don't lose out either way.