I am not sure what your error is, but here is what I do.
1. Open the project in Workbench.
2. Click the Tools menu, highlight Command Prompt, and click.
3. Type your command. For example: clie export myfile.csv. This will export every point in the project.
4. The file is located in the project folder. For example: C:\Program Files\Proficy\Proficy CIMPLICITY\projects\MyProject\myfile.csv.
For further help on the import/export, consult the help file. Search for clie. There are qualifiers you can add to the command to limit the amount of points.
I think if you do not open the command prompt from the project, you will have problems. You must be in the folder of the project. By opening from Workbench, you are automatically located in the proper folder.