The "Duplicate names have been found. The duplicate names have been renamed" message appears when you add a window with the same name as an existing window in the project. This happens, for example if you append a project (File:Append) to an open project, where both projects have a Data1 worksheet window. The Data1 worksheet in the project file that gets appended will be renamed to AData1.If you double-click on the layer icon, in the upper-left hand corner of your graph, to open the Layer Dialog, do you see your functions (F1, F2, etc.) in the Layer Contents. If yes, move them into the Layer Contents. Do they plot correctly?
It may be easier for someone to look at your project and see exactly what is happening. Feel free to email your local Origin Technical Support Rep., attaching your project to the email.