> 1) No, the 2 groups have significantly different values on these covariates (IQ, SES).
This is a very delicate and serious situation! I see that you didn't use option -qVarCenters in your script, which means you're comparing the groups at the overall average IQ and SES across the groups, which may or may not make sense. This may also explain the discrepancy between the 3dMVM output and the ROI data.
I don't know the specifics of your experiment. Are the differences in IQ and SES because of the nature of the subject groups, or due to sampling issues?
Gang