I've never seen this be an issue before now in my career, but it is an option I never even knew was there...
I saw that there was an appearance/attributes difference by selecting both paths at the same time.
In the attributes panel, one of the fills is set as "use non-zero winding fill rule" where the other is set at "use even odd fill rule".
I'm not sure why Onyx recognizes and fills them as slightly different colors though, but people in the links below are experiencing somewhat similar issues with the same feature.
	
	
		
			
				
			
			
				
				I have – what is probably the reverse of a normal problem – I have the answer, but I appear to have just stumbled upon it.  Could anyone explain the background thinking, so that I can get a better grasp of the fundamentals. This would help me in designing future projects.  Firstly in picture A –...
				
					
						
							
						
					
					community.adobe.com
				
 
			 
		 
	 
	
	
		
			
				
			
			
				
				http://www.youtube.com/watch?v=l8uGl6LdV7Q  Above is a video showing the problem.  How can I create a compound path out of several shapes by pressing the keyboard shortcut Ctrl+8 just once?  Right ...
				
					
						
							
						
					
					graphicdesign.stackexchange.com