I am checking on this issue but please open a ticket support will work with you on it.
Andy and I checked on this and our team have not seen this before. So definitely open a support ticket so that we can get it addressed. I'll alert support that you'll be contacting them.
I havent seen this exact issue with system manager not displaying the nodes, but I have seen it where the nodes refuse to delete when doing it from the web interface.
So far from the users I have here attempting it; it appears that it wont delete the nodes from the web interface if your using IE7. This does still work from my other browsers (IE6, firefox, safari) but not IE7.
As for the System Manager not displaying the nodes have you tried to reinstall NPM?