It's strange because I can reproduce it.
I've send you my settings file.

I did some more tests and now I figured out when this happens.
I happens when you start CN minimized to tray. When you kill explorer and restart it, there is no tray icon.
If you open CN one time before you kill explorer, the icon gets restored.

I can reproduce it with Win 7, Win 8, Win 8.1 and now Win 10 all 64-bit.
I use the portable version of CN.
I do exactly the same. kill and restart explorer from Task Manager.

Hey Alex,

I reported the bug in 2009. For me it's still not fixed. Even with version 2.9.3.
Perhaps you can check it again.
CN is currently the only program which doesn't restore the icon when Explorer
gets restarted.