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.NET 4.0 issues

Hello,

I am having an issue with .net framework 4.0. The current setup we have is one server box, and 3 VMs running Server 2008 R2. The priority right now is the AD server, there is also an exchange server and a terminal server. We currently have backup software and remote monitoring programs that require .net to be running successfully. The service won't start, and will give me the error when I manually start it, an error pops up saying:
 "The Microsoft .NET Framework NGEN v4.0.30319_X64 service on Local Computer started and then stopped. Some services stop automatically if they are not in use by other services or programs."

If I perform the .net repair tool from microsoft, it fixes the installer and then the service will start, but needs a reboot. The other programs continue having their issues even with the service started. If I reboot, the problem occurs again.

I have the .net enabled in the server features, and all updates installed.

The part that confuses me is that it does this on all 3 VMs. It seems to me like the issue is .net or somehow windows installer. I do not know what to do from here, so any help will be greatly appreciated! Thank you.
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Ryan McCauley
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Sorry for the late reply,

It ended up being the firewall policies not in the correct order after an update. However it was still only doing this for the servers. Appreciate the help, regardless.