Ok I fixed it; it seems I hit ‘save default settings’ awhile ago and well that caused that .blend file to be what was loaded up when you started up the program or when you start a new project. I fixed it somehow…
This can be deleted
In the event the admins DO decide to keep this for future reference for others:
Clicking ‘Save Default Settings’ while on a project seems to make that project your default blend file when you load up Blender or when you hit ‘new’ under file. However, ‘Load Default Settings’ still defaults to the original little cube for the file>new. So just load up those settings and then save them and you’ll fix it.