You have both disabled. This config works fine, I'm using it for almost forever.
And how do you start a new instance? It definitely doesn't work for me. CB behaves as if I selected only one instance being allowed, and if I have the "use already running" enabled then it just hangs when doubleclicking on a projectfile.
What OS and C::B versions are you using?
Windows 7, CB 13.12 Build Dec 27 2013 12:58:38 - wx2.8.12 (Windows unicode) 32 Bit.
Actually I found another bug related to this. I opened the "Project->rightClick->Build options..." and while this dialog was opened, I double clicked on a project file. The Dialog from the old project stayed open, while the new project was loaded in the main window (still only one instance though).