The interesting part is the .Net version part, because this doesn't directly lead to a change in IIS settings as I understand it, only web.config settings.
This suggests your IIS management console is utterly borfed, which isn't a common occurrence.
I'd suggest any of:
- Disable any antivirus that might be present
- Copy Metabase.XML and check for obvious corruption in a text editor
- Look at the event log to understand possible reasons for service failure
- Hire a good exorcist
IIS Manager essentially edits the in-memory metabase, which gets persisted to Metabase.XML on disk. However, the ASP.Net tab doesn't play in the same space, it typically edits the web.config file (I might not be entirely correct there, there might also be a ScriptMaps implication to the use of the tab), in which case something Really Interesting is happening there.
So, take a snapshot of metabase.xml before changing anything, and perhaps grab a copy when the server fails (assuming it's going to fail at least once before you fix it), and compare them.