Hi Francois,
Thanks for your reply. When you set the significance level alpha to 1, there is still no map of p-values and the result is the same "all values are null".
There is a warning that comes up after running the paired ttest saying "File 2 contains a data matrix that has a different size" - it gives this warning for all the files apart from the first one (File 1). This seems odd to me as I am running the paired ttest on the normalised rectified source-level subject averages as described above.
The Test > Difference of average" works well however and I can see the expected effects.
Thanks again for your insight 
Corinne