What it sounds like you're experiencing is one of several things:
1) The application under test is not running in the same state as a project suite as it is when running as a project.
2) The temporary variables are being initialized differently in the suite than they are as a project.
3) Some other project is altering the temporary variables before the project in question hits them.
In order for us to help you, we need to see more of the JScript code that you're running, how you're assigning the variables, what you are assigning them from, etc. Could you share more project details?
Thanks!