Had the same problem too on my OSX, and partially solved it. Had the latest versions of syntastic (git clone today) and flake8 3.0.4. Vim 7.4.
flake8 ran fine from command line and picked my global ~/.config/flake8. Vim did not output anything if I had the config file, but worked fine without the flake8 config file.
I partially solved the problem by having the flake8 config not in file system but in my .vimrc:
let g:syntastic_python_flake8_args='--ignore=E203,E231'
but this is not the best solution as the config is not shared.
For the initiated developers, when I enable debugging
let g:syntastic_debug = 1
I get this output:
syntastic: 4.516990: &shell = '/bin/bash', &shellcmdflag = '-c', &shellpipe = '2
>&1| tee', &shellquote = '', &shellredir = '>%s 2>&1', &shellslash = 0, &shellte
mp = 1, &shellxquote = '', &shellxescape = ''
syntastic: 4.517587: UpdateErrors (auto): default checkers
syntastic: 4.517927: CacheErrors: default checkers
syntastic: 4.518502: g:syntastic_aggregate_errors = 0
syntastic: 4.518666: getcwd() = '/Volumes/myproject/src'
syntastic: 4.525418: CacheErrors: Invoking checker: python/flake8
syntastic: 4.526113: SyntasticMake: called with options: {'errorformat': '%E%f:%
l: could not compile,%-Z%p^,%A%f:%l:%c: %t%n %m,%A%f:%l: %t%n %m,%-G%.%#', 'make
prg': 'flake8 main.py', 'env': {'TERM': 'dumb'}}
syntastic: 4.727963: system: command run in 0.201426s
syntastic: 4.729751: getLocList: checker python/flake8 returned 1
syntastic: 4.730094: getLocList: checker python/flake8 run in 0.204568s