I tried this and it looks like all my environment variables are being inherited correctly:
$ tcsh
% setenv test val
% echo $test
val
% sh -c 'echo $test'
val
% ipython
In [1]: import os, afni_base
In [2]: os.environ['test']
Out[2]: 'val'
In [3]: com = afni_base.shell_com('echo $test')
In [4]: com.run()
val
Out[4]: 0
In [5]: com = afni_base.shell_com('echo $test', capture=1)
In [6]: com.run()
Out[6]: 0
In [7]: com.val(0)
Out[7]: 'val'
What happens if you patch afni_base.py after line 865 to
print '\x1b[32m%s\x1b[0m' % o
print >>sys.stderr, '\x1b[31m%s\x1b[0m' % e
and try again? (That'll sort-of tee the output, with extra stdout green and stderr red so you can tell them apart from the normal output of align_epi_anat.py)
