Below is my output from set. Unfortunately I have no idea what to make of it. I tried just copying everything from Terminal's set output to .bashprofile but that didn't work. Thanks and I'll look into the spell check stuff.
Here is set from SciTE
>set
BASH=/bin/bash
BASH_ARGC=()
BASH_ARGV=()
BASH_EXECUTION_STRING=set
BASH_LINENO=()
BASH_SOURCE=()
BASH_VERSINFO=([0]="3" [1]="2" [2]="48" [3]="1" [4]="release" [5]="x86_64-apple-darwin11")
BASH_VERSION='3.2.48(1)-release'
DIRSTACK=()
EUID=501
GROUPS=()
HOSTNAME=Christopher-David-Desjardinss-MacBook-Pro.local
HOSTTYPE=x86_64
IFS=$' \t\n'
MACHTYPE=x86_64-apple-darwin11
OPTERR=1
OPTIND=1
OSTYPE=darwin11
PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/texbin:/Applications/Mplus
PIPESTATUS=([0]="0")
PPID=21724
PS4='+ '
PWD=/Users/chris/Dropbox/Documents/university/dissertation/oral_exam_presentation
SHELL=/bin/bash
SHELLOPTS=braceexpand:hashall:interactive-comments
SHLVL=1
TERM=dumb
TMPDIR='/private/var/folders/qc/hcwz29kj0f70tbd3p_k5sdkw0000gn/T/Cleanup At Startup'
UID=501
_=TMPDIR
Here is set from Terminal
chris$ set
Apple_PubSub_Socket_Render=/tmp/launch-ZAz3gE/Render
Apple_Ubiquity_Message=/tmp/launch-rkHSFg/Apple_Ubiquity_Message
BASH=/bin/bash
BASH_ARGC=()
BASH_ARGV=()
BASH_LINENO=()
BASH_SOURCE=()
BASH_VERSINFO=([0]="3" [1]="2" [2]="48" [3]="1" [4]="release" [5]="x86_64-apple-darwin11")
BASH_VERSION='3.2.48(1)-release'
COLUMNS=105
COMMAND_MODE=unix2003
DIRSTACK=()
DISPLAY=/tmp/launch-yyGYS3/org.x:0
EUID=501
GROUPS=()
HISTFILE=/Users/chris/.bash_history
HISTFILESIZE=500
HISTSIZE=500
HOME=/Users/chris
HOSTNAME=Christopher-David-Desjardinss-MacBook-Pro.local
HOSTTYPE=x86_64
IFS=$' \t\n'
LANG=en_US.UTF-8
LINES=51
LOGNAME=chris
MACHTYPE=x86_64-apple-darwin11
MAILCHECK=60
OLDPWD=/Users/chris
OPTERR=1
OPTIND=1
OSTYPE=darwin11
PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/texbin:/Applications/Mplus
PIPESTATUS=([0]="0")
PPID=22009
PROMPT_COMMAND='update_terminal_cwd; '
PS1='\h:\W \u\$ '
PS2='> '
PS4='+ '
PWD=/Users/chris
SHELL=/bin/bash
SHELLOPTS=braceexpand:emacs:hashall:histexpand:history:interactive-comments:monitor
SHLVL=1
SSH_AUTH_SOCK=/tmp/launch-Wek511/Listeners
TERM=xterm-256color
TERM_PROGRAM=Apple_Terminal
TERM_PROGRAM_VERSION=303
TERM_SESSION_ID=97897B1B-42A3-404C-BBCC-395BEBAD4A23
TMPDIR='/private/var/folders/qc/hcwz29kj0f70tbd3p_k5sdkw0000gn/T/Cleanup At Startup'
UID=501
USER=chris
_=.bashprofile
__CF_USER_TEXT_ENCODING=0x1F5:0:0
update_terminal_cwd ()
{
local SEARCH=' ';
local REPLACE='%20';
local PWD_URL="file://$HOSTNAME${PWD//$SEARCH/$REPLACE}";
printf '\e]7;%s\a' "$PWD_URL"