Originally, some file and folder types (eg shared folders) had a shield superimposed over the icon. When I installed dropbox this changed to a green tick (I think). Recently this has been lost - now any such icons are not displayed at all (they are blank).
How can I fix this?
I am perfectly happy to edit the registry, if that's what it takes.
You would only see those overlays on certain files or in certain folders.
Windows also has a limit of 15 overlay icons, and uses the majority of the slots for its own ones. That means everything else that tries to use them has to fight with each other, and it is essentially whichever asks for them first will win. (The limit is per-process, so you may see different icons in different processes.)
Some tools let you configure whether, or which, overlays from them are used. e.g. TortoiseSVN does this.
Others would simply need to be uninstalled, or have their shell extensions disabled to prevent them from using up slots.
The folders you view first may also be a factor, as they may trigger shell extensions to be loaded in a different order.
There are some registry settings which are supposed to influence the order overlay icons are considered, but I am not sure how well they work, or if they work at all outside of Explorer itself.
Not relying on icon overlays at all is another possibility in some cases. If you can define a filter in Opus which matches the files you want overlays to be on, then status icons or colored labels can be used instead, and those are unlimited.