Kris,
My guess is that you were runing the two analyses with two different versions of AFNI on your Mac and Linux. The one on your Mac is more recent with the Legendre polynomials as a model for baseline while the older versions adopted simple polynomials. For straightline moedeling of the baseline, the two are essentially the same thing although their coefficients look different. And apparently the results on the manual were from an older version of 3dDeconvolve. So don't worry about it.
Gang