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=5.0.0.0″
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
http://blogs.msdn.com/b/devkeydet/archive/2015/02/17/debug-crm-online-plugins.aspx
Hope it helps..