Hi Matt,
Would you mind posting a sample of one of the timing files that is not giving you the number of betas that you expect? Or, you could mail me the timing file along with any X.xmat.1D file (or a nocensor version).
Are you using afni_proc.py? If so, try adding -regress_compute_fitts. That will use 3dcalc to compute the fitts, rather than having 3dDeconvolve (use the extra RAM to compute and) write it out.
While 16 GB seems like plenty for this, if other programs (like web browsers) are using all of the RAM, you might have to close some programs.
- rick