This page describes the bug in FSFAST in which the contrasts created from the mkanalysis-sess GUI are incorrect because they were not normalized correctly.
The most serious repercussions are for unbalanced contrasts, ie, contrasts that have an uneven number of positive and negative components. For example, if you had three conditions E1, E2, and E3, and you wanted to test E1 vs (E2 + E3), you would hit 'Add Contrast' in the mkanalysis.gui window to bring up the contrast window. You would then hit the green button under "A" next to "Condition01", and the red buttons under "C" for "Condition02" and "Condition3". The contrast matrix should be [1 -0.5 -0.5].
This does not affect contrasts
For balanced contrasts