Hi Sven,
That seems like a problem with line wrappers (e.g. some
line in 3dDeconvolve does not end with a '\').
What version of afni_proc.py are you using?
(afni_proc.py -ver)
Please feel free to email your script to me directly, since
only .jpg files can be attached (put the mouse over my
"Author" name for the address).
- rick