A follow-up, it definitely appears to be an identifier code issue. I used 3dCalc to 'convert' the filtered_data to AFNI BRIK format (-a data -expr 'a') and this altered the identifier code. I was then able to run InstaCorr with no issues.
I'm still relatively new to AFNI, is there somewhere it would give a warning that multiple 'identical' datasets were detected? It did provide warnings that the files had "dimensions altered since AFNI extension was added" but I wasn't certain what to make of that.
