I'm getting a strange behavior of checkboxes inside NSPopover on OS X 10.10.3.
Colors of checkboxes are distorted but other elements like regular buttons or labels have correct colors.
Top image: how NSPopover renders in a running app (black background is from another app).
Bottom image: NSPopover view in Interface Builder.
Visual Effect Views (like used in NSPopover) are totally messed up in OS X Yosemite. Luckily they are working fine now in El Capitan.
A workaround on Yosemite should be to set the appearance
property of each checkbox, label, scrollView etc. to NSAppearanceNameAqua