I found time to check on this first issue - changing the AFNI_COMPRESSOR environment variable in the .afnirc such that it was commented back out again fixed things. I now have lovely ETAC output. Setting the AFNI_COMRPESSOR to nothing right before running my etac script (aka export AFNI_COMPRESSOR=; tcsh cmd.etac,pain_on_brain) also worked just fine, and does not require any .afnirc editing.
The second issue still remains, data think they are 'orig', which can be corrected by running 3drefit afterwards - not sure what could be happening there. This is with the most updated version of AFNI (updated today). No sign of any warnings of anything that explain why orig space is being used for output...
To end on a positive note, the 5percent files are produced now, albeit it with the warning that some were not available.