(1) As Rutvik Desai pointed out, were your two "scans" really two runs (subjects remained in the scanner) or two sessions (subjects got out of scanner in between)?
(2)
> The reason we feel that that the results are off, is that the two
> analyses produce drastically different results for conditions in the
> first scan.
Drastically different results between the two analyses for same conditions of the 1st run with same subjects?
(3) Your 3dDeconvolve script failed to show up. Try copy & paste.
Gang