Recently I had an unusual case where customer called in with a problem that he could see none of the web sites in the left side connection pane but all of the sites worked as expected and could be accessed in the middle pane when selecting sites folder in the connections pane. I had not seen a case with these symptoms before and when I searched prior cases and the web, I did not find much, the closest was a question on stackoverflow.com but there was not any answers that resolved the problem. Everything I found was not resolved. We tried removing IIS management and reinstalling it then we removed anti-virus software but neither action fixed the problem.
I discussed this with one of my associates and he had seen this before and suggested that we move the sites element. He noted that sites element must be </log> and <webLimits/> or the sites may not be seen in IIS manager.
Moving the sites element to this location resolved the problem. This is what we had before moving sites element:
Here is where the sites were in the original config file. I used a text editor so to see the line number.
This is where the sites needed to be.
So, we edited the config file and moved the sites like this.
With <webLimits/> is just after the sites closing tag.
My teammate who has seen this before says that sites must be </log> and <webLimits/> or the sites may not be seen in IIS mgr. He had seen this before but, in that case, they were using a script to add new sites and the script was putting the sites in the wrong area.