I ran into this issue last week when trying to clean up individuals ACLed to the Farm Administrators group.  When I attempted to delete this one user, SharePoint threw up the default error page with '1387' on it.  Nothing more to the error message just 1387.  Digging into this I found that the user no longer existed in Active Directory and had been off the project for some time.  My first thought was that the delete through the UI had some checks to make sure that user existed, so I decided to attempt the delete through the OM; same error but I did get a stack trace.  I am sure if I had set callstack, CustomErrors to true, I would have saw the same trace, but I like to code.  The stack trace revealed that the remove user from Farm Administrators process, eventually calls the RemoveMemberFromLocalAdministrationWorkerProcessGroup methof which uses Win32 API calls to remove the user from a local group on the server.  This is what is throwing the error and cannot be cleaned up using the API.  To solve this I needed to add the user back to AD,remove it from the Farm Administrators group and remove it from AD.