Syntastic for Vim only works on GuiEnter or switching of buffers. When I write a file the location list is empty. How do I debug this?

Question

I want to preface by saying that I'm quite inexperienced with vimscript, so please bear with me. When I run SyntasticInfo I get the following:

Syntastic version: 3.7.0-199 (Vim 704, Windows)
Info for filetype: python
Global mode: active
Filetype python is active
The current file will be checked automatically
syntastic: error: checker output:
syntastic: error: checker python/python: can't parse version string (abnormal termination?)
Available checkers: flake8 pep8 pycodestyle pyflakes
Currently enabled checker: flake8

I have a suspicion that it has something to do with my shell var in my vimrc but I cannot figure out why it works when I first open an instance of gvim and on buffer switch.

Below is my vimrc:

"bundle management
set rtp+=$HOME\vimfiles\bundle\vim-colors-solarized
set rtp+=$HOME\vimfiles\bundle\syntastic
set rtp+=$HOME\vimfiles\bundle\SimpylFold
set rtp+=$HOME\vimfiles\bundle\vim-python-pep8-indent
set rtp+=$HOME\vimfiles\bundle\vim-flake8
set rtp+=$HOME\vimfiles\bundle\AsyncCommand

set nocompatible
filetype plugin indent on
syntax on
color solarized
autocmd BufEnter * silent! lcd %:p:h
"browse vert diffsplit
behave xterm
set expandtab
"set shell=powershell.exe\ -ExecutionPolicy\ Unrestricted
"\ -windowstyle\ hidden
set shell=cmd
set shellcmdflag=/c
set noshellslash
set shellpipe=>
set shellredir=>
set smartcase
set showcmd
set winaltkeys=no
set viminfo='100,f1,n$USERPROFILE\\_viminfo.txt
set lines=86
set columns=240
set mousemodel=popup
set clipboard=autoselect
set noswapfile
set autoread
set autowrite
set iskeyword+=.
set iskeyword+=&
set iskeyword+=$
set iskeyword+=%
set iskeyword+=:
set fileformats=dos,unix
set backspace=indent,eol,start
set ts=3
set autoindent
set ruler
set ignorecase
set number
set hlsearch
set modeline
set modelines=29
set guifont=Lucida_Console:h11:cANSI
set complete-=k complete+=k
set omnifunc=syntaxcomplete#Complete
set encoding=utf-8
set wildmenu
set wildmode=list:longest,full

""bad white space
highlight BadWhitespace ctermbg=red guibg=darkred
au BufRead,BufNewFile, *.c,*.h,*.sas match BadWhitespace /\s\+$/
"syntastic var
set statusline+=%#warningmsg#
set statusline+=%{SyntasticStatuslineFlag()}
set statusline+=%*

let g:syntastic_enable_highlighting=1
let g:syntastic_always_populate_loc_list=1
let g:syntastic_auto_loc_list=1
let g:syntastic_check_on_open=1
let g:syntastic_debug=8
au BufRead, *.py let g:syntastic_debug_file = "~/syntastic.log"
let g:syntastic_check_on_wq=0
let g:syntastic_python_checkers=['flake8']
let syntastic_nested_autocommands=1

"saves and loads folds in files that have them
au BufWinLeave * silent! mkview
au BufWinEnter * silent! loadview

augroup sascode
   au GuiEnter,BufEnter *.sas,*.log,*.lst    set makeprg=sas\ -nosplash\ -sysin\ %\ -log\ %:r.log\ -print\ %:r.lst
   au GuiEnter,BufEnter *.sas,*.log,*.lst,*.tcl    set ff=dos
   au GuiEnter,BufEnter *.sas,*.log,*.lst,*.tcl    setf sas
   au GuiEnter,BufEnter *.sas,*.log,*.lst,*.tcl    set lines=86 | set columns=240
   au GuiEnter,BufEnter *.sas,*.log,*.lst,*.tcl    color solarized
   au GuiEnter,BufEnter *.sas,*.log,*.lst,*.tcl    syntax on
   au GuiEnter,BufEnter *.sas,*.log,*.lst,*.tcl    set autoindent
augroup END

"Declare local buffer variables when entering a buffer if not already defined
au BufEnter,BufReadPost *.py,*.sas,*.lst,*.log call SetBVars("false")
au BufFilePost *.py,*.sas,*.lst,*.log call SetBVars("true") "after saveas command reset buffer vars

function! SetBVars(reset)
    if !exists("b:fileRoot") || a:reset=="true"
       let b:fileRoot = expand("%:p:r")
       let b:ssas     ='"'.b:fileRoot.'.sas"'
       let b:slog     ='"'.b:fileRoot.'.log"'
       let b:slst     ='"'.b:fileRoot.'.lst"'
       let b:sbat     ='"'.b:fileRoot.'.bat"'
       let b:spy      ='"'.b:fileRoot.'.py"'
       let b:sas      =b:fileRoot.'.sas'
       let b:log      =b:fileRoot.'.log'
       let b:lst      =b:fileRoot.'.lst'
       let b:bat      =b:fileRoot.'.bat'
       let b:py       =b:fileRoot.'.py'
    endif
endfun

au BufRead,BufNewFile *.ps1 set filetype=PowerShell
au! Syntax PowerShell source $HOME\syntax\ps1.vim

augroup XML
   au GuiEnter *.xml,*.XML    color solarized
   au GuiEnter *.xml,*.XML    set ts=3
   au GuiEnter *.xml,*.XML    setf xml
   au GuiEnter *.xml,*.XML    set ff=dos
   au GuiEnter *.xml,*.XML    set shiftwidth=3
   au GuiEnter *.xml,*.XML    set lines=80 | set columns=190
augroup END

augroup scripts
   au GuiEnter *.pl,*.sh,*.js,*htm,*.bat     :set makeprg=perl\ %
   au GuiEnter *.pl,*.sh,*.js,*htm,*.bat     color solarized
   au GuiEnter *.pl,*.sh,*.js,*htm,*.bat     set ts=3
   au GuiEnter *.pl,*.sh,*.js,*htm,*.bat     set ff=dos
   au GuiEnter *.pl,*.sh,*.js,*htm,*.bat     set shiftwidth=3
   au GuiEnter *.pl,*.sh,*.js,*htm,*.bat     set lines=60 | set columns=190
augroup END


augroup textfiles
   au GuiEnter *.txt,*.TXT    set wrapmargin=10
   au GuiEnter *.txt,*.TXT    color solarized
   au GuiEnter *.txt,*.TXT    set textwidth=130
   au GuiEnter *.txt,*.TXT    set lines=70 | set columns=220
   au GuiEnter *.txt,*.TXT    set autoindent
augroup END

augroup config
   au GuiEnter .profile,*rc      color solarized
   au GuiEnter .profile,*rc      set lines=60 | set columns=140
augroup END