Mmmmmh, your problem might be cause by one or more things..
1.- When you create the shortcut to the Tweak Sub file, you must edit the targeting Properties of the shortcut, adding "Wolfie" at the end of it.
2.- When you want to change the loadout, first you select a sub, then you select a year and then you change the loadout for the torps 1 by 1 or all at the same time with the option "Change All". After that, you must click on "Save" or on "Save for All Years". Normally, this should work.
3.- Make sure that there is no "copy of basic.cfg" file created in the same directory, if there is, then delete it.
4.- Make sure that the type of torp you are selecting is available when doing the same for other types of torps. Anyway, I think the tweak pack takes care of it....
5.- If all this fails, then you can change the loadout manually opening the basic.cfg file, located in SilentHunterIII\Data\Cfg Go for the loadout section for the sub you want to change and replace the number with 2 like (example only):
[SUBMARINE_AMMO2]; VIIB
.
.
.
Year0=1939
ForeTube00=2
ForeTube01=2
ForeTube02=2
ForeTube03=2
ForeResIntern00=2
ForeResIntern01=2
ForeResIntern02=2
ForeResIntern03=2
ForeResExtern00=2
ForeResExtra00=2
ForeResExtra01=2
AftTubes00=2
AftResIntern00=2
AftResExtern00=2
Z01_00=3 ; VIIB/1
M01_00=1
A01_00=8
SuperCharger_00=-1
Snorkel_00=-1
Batteries_00=1265
AftBatteries_00=1265
Hydrophone_00=1270
Sonar_00=-1
Radar_00=-1
RadarWarningReceiver_00=-1
Decoy_Launcher_00=-1
SonarCoatings_00=-1
RadarCoatings_00=-1
Renown0=0
I hope this helps you... 
Let me know if you need more help and if this worked or not.
There are some other things that can be done, but first let me know about this.
CapZap