If you are using custom icon replacements, as in putting your own tga files into Interface\ICONS, the EquipmentManager icon selector will fail to set a correct icon path for every spell whose icon you are trying to use and fall back to the question mark icon.
Video:
https://dl.dropboxusercontent.com/s/..._09-18-35.webm
(I am using an addon in the video that expands the icon selection screen, but the problem happens without any addons, too)
Example of such a icon pack:
http://www.wowinterface.com/download...nPackBlue.html