SCOM 2016 agent causes issues with IIS .Net 2.0 Application

As many other blogs and users have posted SCOM 2016 Agent currently has an issue with servers that are running IIS using .net 2.0 apps.
One thing we have noticed in our environment recently is you don't always see errors with the agent causing the service to crash.
Sometimes the app just doesn't work as it is supposed to. When troubleshooting an issue with IIS site using 2.0 try and uninstall the SCOM agent and see if that resolves the issue.

If it does then follow the recommended resolution steps below, we typically install using the NOAPM=1 setting.

Summary
APM feature in SCOM 2016 Agent may cause a crash for the IIS Application Pool running under .NET 2.0 runtime.
Cause
Several callbacks within APM code of SCOM 2016 Agent utilize memory allocation that’s incompatible with .NET 2.0 runtime and may cause an issue if this memory is later accessed in a certain way. Those particular modifications were added in SCOM 2016 Agent and are not present in SCOM 2012 R2 Agent.

Resolution
The fix for this issue is to be provided with SC 2016 OM Update Rollup 3. The aforementioned code paths will not be executed if the Application Pool is running under .NET 2.0 Runtime. We are also evaluating to release a hotfix for this issue.
Workaround
There are several workarounds for this issue:

• Application pool can be migrated to .NET 4.0 Runtime;
• SCOM 2016 Agent can be replaced with SCOM 2012 R2 Agent, it’s forward-compatible with SCOM 2016 Server and APM feature will continue to work with the older bits;
• SCOM 2016 Agent can be reinstalled with NOAPM=1 switch in msiexec.exe setup command line, APM feature will be excluded from setup;