I just repurchased the game from GOG as well and had a similar problem until I realised that the "Installed To" string in the registry was set to a "." instead of the correct path. Once I corrected that the Config Manager was able to install mods correctly.
I just ran Regedit, then went to "Computer\HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\Microsoft\Microsoft Games\Close Combat\3.00" and looked for the "InstalledTo" string. Changed it to the path where CC3 was installed and all was fine.
In August of 2004, Zappi, Homba, Bambam887, RedScorpion and MOOXE all pitched
in to create this Close Combat site. I would to thank all the people who have visited
and found this site to thier liking. I hope you had time to check out some
of the great Close Combat mods and our forums. I'd also like to thank
all the members of our volunteer staff that have helped over
the years, and all our users that contributed to this site!