I have a server HP ML350G5 on which I had an installation of nomachine freenx 3.5.0
Do you mean NoMachine Free Edition 3.5.0 or freenx from freenx? I’m asking because they are very different software. I don’t know what freenx may have changed in your environment but for sure NoMachine 4 handles the upgrade from NoMachine 3 in a way that has demonstrated to be quite seamless for most users. Additionally I have really no idea of what NoMachine 4 may have changed in your environment, since NoMachine 4 doesn’t change ANYTHING in the user’s environment, except starting whatever desktop environment you may have configured, pointing it at a different X server. Bug or unintended side effects excluded, of course.
One can be this:
https://www.nomachine.com/AR02L00776
There is a TR for this problem:
https://www.nomachine.com/TR12K04127
The solution is being released today as part of the 4.1.
About the machine not starting on the physical X server I don’t have any idea. I suggest you check if the article applies to your case and then try to start the X server on the command line without loading any desktop environment.
If the X server loads, you can try some simple X clients, like xterm. Post the results here, so that we can start from there.