Here's a faster, Open Source alternative to the CodeX tool: https://github.com/fritzw/cube-utils
Feel free to try it out and play around with it. It works on Windows, Linux, and Mac OS X. It's a simple command line app but can also be used by just drag-and-dropping a .bfb-file onto the encoder.
You can also use it in the Scripts tab in Simplify3D to automatically convert the .bfb file to .cubepro or .cubex.
Back story:
We've recently purchased Simplify3D because the CubePro printer which my institute owns is listed as "Supported" in the printer compatibility tool. However, Simplify3D doesn't output the binary .cubepro files which are the only things that this printer understands. There is only that dubious CodeX tool (mentioned in "Tip of the day 30" with a broken download link for 64-bit Windows), which is quite slow on Windows and horribly slow on Linux and Mac. So I took a look at the CodeX tool and the .cubepro file format and found out that it only does a Blowfish ECB encryption of the .bfb file.
Cheers,
Fritz