There is no fixed upper limit to the size of a data table in 3dttest++, so I'm not sure what's going on here.

Is this block below a direct copy of the output, without edits?

++ loading covariates
100408' in covariates file '
101006' in covariates file '
101107' in covariates file '

These messages are supposed to be in the form

** ERROR: Can't find label '100408' in covariates file

So if the messages you gave are exactly as you see them, I guess that the covariates file contains some special character, probably a carriage return (CR) that is both messing up the string matching (i.e., finding which row to use in the covariates table for each dataset), and messing up the formatting of the error messages. If this is the case, then a command like

file_tool -show_file_type -infile OLD.txt -prefix NEW.txt

might fix it up.