In the old window where I manually set the path etc. this is the output of the check
Things only work in the new window when I set the path manually again (but still the same library error).
Thanks ever so.

afni_system_check.py -check_all
============ afni_system_check.py version 0.6, March 14, 2014 ============

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 13.1.0
version: Darwin Kernel Version 13.1.0: Thu Jan 16 19:40:37 PST 2014; root:xnu-2422.90.20~2/RELEASE_X86_64
distribution: 10.9.2 x86_64
number of CPUs: 4
apparent login shell: bash

--------------------- AFNI and related program tests ---------------------
which afni : /Users/NEURO-222/afni/afni
afni version : Precompiled binary macosx_10.7_Intel_64: May 1 2014
which python : /usr/bin/python
python version : 2.7.5
which R :
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/NEURO-222/afni/afni)
R : 0
python : 1 (/usr/bin/python)

testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : FAILURE
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Users/NEURO-222/afni/3dAllineate
Reason: image not found
3dRSFC : success
SurfMesh : success

checking for $HOME files...
.afnirc : missing
.sumarc : missing
.afni/help/all_progs.COMP : missing

------------------------------ python libs -------------------------------
---------------------------------------------------------
** python module not found: PyQt4

-> please see the output of "uber_subject.py -help_install"


------------------------------- path vars --------------------------------
PATH = /usr/local/bin:/usr/local/bin:/Applications/y/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Users/NEURO-222/afni:/Users/NEURO-222/afni

PYTHONPATH =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH = /Users/NEURO-222/afni


------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing suma_demo
atlas : found TT_N27+tlrc under /Users/NEURO-222/afni

------------------------------ OS specific -------------------------------