Hi, Dante-
Like Antaeus of old, run-ins with hideous details just (counterintuitively, perhaps) make AFNI programs stronger!
I ran your commands with different data (the FATCAT_DEMO data), using a weights file of all ones, and things went fine---the correlation values were unchanged from the original. So I wonder if the issue you are seeing is particular to that data in particular---what does the *.1D file of weights look like? Note that the diagonals of the "CC" (Correlation Coefficient) matrix should always be 1s, because the correlation of a time series with itself is unity.
--pt
