afni.nimh.nih.gov

The regressors form the columns of the X-matrix, which are
regressed against each voxel time series. So the regressors
need to be TR-locked against the data, having the same number
of values/TRs.

That is to say your regressors should be on a 2-second grid.

3dDeconvolve expects this, and so looks at only the first 256
values in your regressors, which are all zero for those two
regressors.

- rick