The older version of 3dDeconvolve would just ignore any 'extra' information after the first number present in each blank-delimited string when input to -stim_times. The new version is pickier, which is why your timing file worked on an older edition of 3dDeconvolve and failed on the newer one.
This change was made when I unified the input functions for reading data for -stim_times and the various other options in the same -stim_times_XXX class.