I have a sneaking suspicion that NanoFXv2 Beta was only extracted from the BCMI.net file, like you would extract a folder from a WinZIP file. However, I cannot be 100% sure of this since I havn't used BCMI since I got BCUT.
I only make this suggestion because BCUT only unpacks NanoFXv2Beta. It doesnt install it for you. You would have to navigate to the BC root folder, located a new folder called 'NanoFX 2' or something of the like, go into it, highlight the folders and then click 'Copy' inside the Nano FX2' folder, then return to the BC root directory, right-click on an empty area somewhere that hasn't got a folder, click 'Paste' and say yes when asked to overwrite the files.
So I suspect that BCMI uses a similar method.