I have an issue recently where we're running into this limitation (server name is fully qualified, and NAME is blank in the INI file, the agent will be created using the name of the server).
The error we're getting when starting the agent is:
U2000041 Invalid LogMessage-call
Note: This has already been resolved by either specifying a name in the INI file, or make the server not use the fully qualified name (or server name is less than 32 characters if NAME is blank in INI).
Has anybody else run into this limitation, and what error message did you get?
Also, note that the error U2000041 Invalid LogMessage-call has many causes as well and does not necessarily mean you're hitting this limitation. This error could be because of missing parameters in ini file, ucxxxxm still running in the background, etc.