We've created a test version which will create a diagnostic file that may let us see what's going on.
If you'd like to try it, you can download it from gpsoft.com.au/files/Opus11/ ... stall2.exe - just install it over the top of your existing install. Once you have installed it (and rebooted if necessary), go to Settings / Preferences / Miscellaneous / Advanced and turn on the debug_icon_data option.
Then, find a file or folder with a missing icon, and simply right-click it. With the debug_icon_data option turned on, right-clicking a file or folder will cause a text file to be saved to your desktop with information about its icon (the context menu itself won't appear). Once you've done this on a couple of different items, turn the debug_icon_data option back off to return to normal.
Then zip and email the diagnostic files to leo@gpsoft.com.au.
Unfortunately we can't reproduce this issue ourselves, but if you can help us by sending these diagnostic files we may have a better chance of working out where the issue lies.