afni.nimh.nih.gov

You have 17 stim_file options. So if 3dD is generating a 35
column matrix, that leaves 18 for baseline. This suggests
your runs.1D file lists 3 runs, not 2.

What does runs.1D look like?

Once you get that straight, consider using symbolic glts,
instead of writing out the ugly matrix format.

Search for 'gltsym' in the page:

[afni.nimh.nih.gov]

- rick