I'm not surer if the alternate start is a bug or intended, but whenever it occurs I encounter a bug where selecting the option to quit and delete save doesn't result in a deleted save. Deleting all files in the /user folder returns the regular Revision 17 start, however the non-deletion of savegame continues. Reinstall of Cogmind returns the Rev 17 start scenario and also functioning quit and delete save, until the alternate start occurs again.
The only modification I have made is to run the game as administrator (win 7 pro 64-bit), if I don't run as admin the game won't save my configuration options.
I have included a picture of how the alternate start looks.