I've just updated a custom DLL written in C# and when I update the reference to the DLL, all of the script method are missing in the Object Explorer view. I can click on the script in the Solution Explorer and all of the methods will come up.. When I go to the Script Configuration, all methods are gone.
If you've created a custom DLL, then you would make sure that your methods are public. If they are not static methods, then you also need to make sure your object with your code is a component.
If you are referring to a script, then there must be something wrong with your script. I would try entering the C# into a new script in a new solution to first make sure that it works. If it does, then perhaps there's some corruption of your script container (I haven't seen that happen recently, but it has happened before, particularly in older versions). What do you mean by script configuration? Perhaps some screen shots would be helpful to illustrate your issue.
The methods you added in your script aren't added to Object Explorer in the "Script Configuration" dialog. Public methods from your script just appear in Object Explorer once you have validated your script. They will never show up in that dialog.