If you have the mods installed properly and they work as the should without Commander, then Commander itself shouldn't make any difference.
The one thing I can think of to start is that you don't have 'Auto Rollback' set in Commander's functions. From the User Guide:
"In order to avoid any potential file integrity problems, it is imperative that you
ALWAYS perform a rollback BEFORE:
· enabling or disabling any mods, either via JSGME or manually;
· uninstalling or reinstalling Silent Hunter III;
· uninstalling SH3 Commander."
One of the funtions in the General Settings part of Commander is "Rollback automatically after exiting SH3." You should always have this box checked unless you are creating mods for SH3. If you don't have the box checked then mods you have activated in SH3 might be shut off when Commander boots up.
Try that as the first step. If it doesn't work then we'll look at the next possibility.