I ran into an very odd variant of an issue. I had a Windows program using shell overlay icons that were not appearing in windows explorer. What makes this odd is that they WERE showing in some "Save" and "Save As" dialog boxes (MS Office and Firefox), but weren't in others (Chrome). I had checked all the normal things, such as making sure the icons appeared first in the
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\ShellIconOverlayIdentifiers
registry key. I looked at the WOW version as well. I even checked the DPI settings as suggested in this question: TortoiseSVN shell overlays only showing for medium and large icons in explorer
None of those worked, but I finally figured it out so I thought it would be nice to put up in case someone else is tearing their hair out over this. The system I ran into this on is Windows 10 and I haven't tested against older versions of Windows.