'gq' not working as expected in Vim 7.3

This was previously working well, but is no longer. I use vim (v7.3)
on my Mac and as my editor on mutt.

Now when I use 'gqG' or 'gq}' when replying to a message in mutt, it
no longer respects the reply '>' characters and wraps everything in
one big glob when I'm just trying to wrap excessively long lines.

Below is my .vimrc file content:


" We use a vim
set nocompatible
set paste
"
" Colo(u)red or not colo(u)red
" If you want color you should set this to true
"
let color = "true"
"
if has ("syntax")
if color == "true"
" This will switch colors ON
so ${VIMRUNTIME}/syntax/syntax.vim
else
" this switches colors OFF
syntax off
set t_Co=0
endif
endif
"set textwidth=75
set autoindent
set tabstop=8
set expandtab
set shiftwidth=4
filetype indent on
"The below is something recently added
"set comments=s1:/*,mb:*,ex:*/,://,b:#,:%,:XCOMM,n:>,fb:-
"set comments=n:>,n:\|
set comments=nb:>

"macro for stripping signatures from mails in mutt
map _qs G?^><CR>?^> -- $<CR>d}
"
" -------------------------------------------
" Commands for quoting URLs in emails
" Copyright (c) 2001-2004 Hugo Haas
" 2004-06-01 version
" I hereby put this code in the public domain.
" Documentation at: http://larve.net/people/hugo/2001/02/email-uri-refs/
" --------------------------------------------

" Insert a reference at the cursor position
function InsertRef() abort
let l:ref = input("Reference: ")
call AskNumber()
set paste
if (col(".") == 1)
execute "normal i[\<C-R>r]\<ESC>"
else
execute "normal a[\<C-R>r]\<ESC>"
endif
normal G
?^-- $
execute "normal O " . @r . ". " . ref . "\<ESC>`rf]"
set nopaste
let l:a = col(".")
normal $
let l:b = col(".")
if ( l:a == l:b )
startinsert!
else
normal `rf]l
startinsert
endif
endfunction

" Convert <http://example.com> into a reference
function ConvertToRef() abort
call AskNumber()
set paste
execute "normal cf>[\<C-R>r]\<ESC>G"
?^-- $
execute "normal O \<ESC>"
execute "normal a\<C-R>r. \<ESC>px0f.2 x`r"
set nopaste
endfunction

" Ask a reference number
function AskNumber() abort
if !exists("b:refNumber")
let b:refNumber = 0
call FindRefHiNumber()
endif
let b:refNumber = b:refNumber + 1
let l:number = input("Reference number (" . b:refNumber . "): ")
if ( l:number != "" )
let b:refNumber = l:number
endif
let @r = b:refNumber
endfunction

" Find the highest number in the text
function FindRefHiNumber() abort
normal 1G
/^$
let l:body = line(".")
let l:cur = l:body + 1
let l:found = 0
let @/="\\[[0-9]\\+\\]"
while ( l:cur <= line("$") )
if (match(getline(l:cur), @/) != -1)
let l:found = 1
break
endif
let l:cur = l:cur + 1
endwhile
if ( l:found == 0 )
let b:refNumber = 0
normal `r
return
endif
" Find the highest number
normal n
let l:l = line(".")
let l:c = col(".")
while (1)
if ( line(".") > l:body )
normal f]mqF[ly`qf]
if ((@0 + 0) > b:refNumber)
let b:refNumber = @0
endif
normal n
endif
if ( (line(".") < l:body) || ((l:l == line(".")) && (l:c == col("."))) )
break
endif
endwhile
normal `r
endfunction

imap <F5> <ESC>mr:call InsertRef()<CR>
nmap <F6> F<mr:call ConvertToRef()<CR>

nnoremap y "+y

" ~/.vimrc ends here


Any help is greatly appreciated!

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