Thanks Rick!
This makes so much sense! I guess what I have seen is that the generated procs look different between resting state and task based analysis since there usually are no regressors of interest in the resting state paradigm. Then afni_proc.py generated a command 3dTproject on the X.mat instead of running 3dDeconvolve (i.e. -x1D_stop in 3dDeconvolve and running 3dTproject after). Does that sound about right?
This explains why the errts.file never got generated with I copied the 3dDeconvolve command from my resting state script!
Thank you :)