While modifying an existing Lotus Notes MA, it does not appear that the Notes MA is communicating with the Notes client. 
Creation of the MA is not a problem, just modifying it after creation.

Work around

A work around for this unusual behavior is below:
  1. Create and configure a Lotus Notes management agent
  2. Exit out of the ma creation
  3. make a connection utilizing the Notes agent Connections tab
  4. make your necessary changes
  5. save your changes
This should resolve the console hanging upon modifying an existing Lotus Notes ma.