I will also try to take a shot at what you mean.
Suppose a design had two variables A and B and the runs look like this:
A B
100 1
100 2
200 1
200 2
150 1.5
Now in conducting these trials, on the first run, you did not achieve A=100. Instead, it was A=95. So, typically the recommendation is that you change the 100 to a 95 before analyzing the data. Why? Because you want to analyze what the actual data were, not what you intended.
If you are very far away from the design point, it will likely affect the analysis. It should! Your first question would be why are you so far away from the intended design point?
Note that @statman is correct on the coding, and if JMP created the design it adds a column property to automatically code to the -1, +1 scale. However, the coding is based on the design levels. If you are quite a ways off, the default JMP coding may not be appropriate and should be modified by editing that Coding column property.
Dan Obermiller