The most common cause of the "machine agent" appearing in the Controller UI but no .NET node appearing in the Flow Map is that no Business Transaction traffic executed on the node in the selected time range.
If this is IIS, make sure that there is HTTP traffic running through it.
In the case where the .NET application executes logic that's not triggered by web traffic, it's typically necessary to define one or more entry points for custom Business Transactions.
Regard,
Brian Wheeldon