On clicking Start Execution button in Plugin Registration Tool for profiling I was getting the AppDomain Unloaded error.
On opening up the error detail the message was
“Could not load file or assembly Microsoft.Xrm.Sdk, Version=126.96.36.199″
Updating the Plugin Project to use the Version 6 assembly that was part of the SDK, from which I was using Plugin Registration tool fixed the issue.
To understand more check the below links
Hope it helps..