Because Page Options will override Theme Options.
With loop pages as single post you should use Theme Options to make it first.
In this case you choose black logo in Theme Options like this: http://prntscr.com/lwab55
And result at frontend: http://prntscr.com/lwab8e
And with pages not loop (Example only homepage)
You can set logo in Page Options like this: http://prntscr.com/lwabo8
Hope you can understand about this.