For anyone who has been following this thread and would like to know the cause of the problem and the resolution provided by Bigboywooly.
I had installed the "SH3Cmdr32" package "as was" so that
should have been OK. However, a thought occured. I forgot that I had installed a "all weapons" mod and it is the only mod' that I have that has a "flottilla cfg" file. I had pasted it in AFTER installing the "GWX3 Gold
& SH3Cmdr32" packages. Unfortunately, it was for SH3 stock version not GWX3 and so it replaced some of the essential flotilla settings and was responsible for the problems I experienced.
The fix was to replace the basic cfg and flotilla cfg in SH3 with the GWX3 Gold versions and all is well. For the extra ammo (if required) the GWX3 basic cfg can be modified before installation.
So that is it. All is well again.