Just to reply to my own question, I mostly got it working. Using the current version of FSL in the default location fixed the errors (apparently the path warnings are not critical). I have an older version (5.0.6) in a non-standard location which the scripts didn't seem to like.
Octave still doesn't work, it fails at fix_3_clean.m, line 30, column 9.
The compiled scripts work, only i noticed in the log that TR is not correctly set. This is set in hcp_fix (fslval $fmri pixdim4). Somewhere in the pipeline scripts the value gets changed - I checked, it's not in the dicom to nifti conversion. Other folks might want to double check this is correct.
Cheers.
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