I've done some more testing on this. Building firefox-1.0.4 with the attached 
build script should produce a copy of firefox in /usr/lib and make a symbolic 
link pointing at it from /usr/bin. Running firefox and then trying to open a 
second instance will open the new url in the current window. The solution is to 
replace the /usr/lib/firefox/firefox script with the attached firefox script. 
This will open a second instance of firefox in a new window (can be changed to 
a new tab by editing line 188). Hope this helps
#!/bin/sh
#
# The contents of this file are subject to the Netscape Public License
# Version 1.0 (the "NPL"); you may not use this file except in
# compliance with the NPL.  You may obtain a copy of the NPL at
# http://www.mozilla.org/NPL/
#
# Software distributed under the NPL is distributed on an "AS IS" basis,
# WITHOUT WARRANTY OF ANY KIND, either express or implied. See the NPL
# for the specific language governing rights and limitations under the
# NPL.
#
# The Initial Developer of this code under the NPL is Netscape
# Communications Corporation.  Portions created by Netscape are
# Copyright (C) 1998 Netscape Communications Corporation.  All Rights
# Reserved.
#

## $Id: mozilla.in,v 1.5 2004/06/01 17:29:53 mconnor%myrealbox.com Exp $
## 
## Usage:
##
## $ mozilla [args]
##
## This script is meant to run the mozilla-bin binary from either 
## mozilla/xpfe/bootstrap or mozilla/dist/bin.
##
## The script will setup all the environment voodoo needed to make
## the mozilla-bin binary to work.
##

moz_pis_startstop_scripts()
{
  MOZ_USER_DIR=".firefox"
  # MOZ_PIS_ is the name space for "Mozilla Plugable Init Scripts"
  # These variables and there meaning are specified in
  # mozilla/xpfe/bootstrap/init.d/README
  MOZ_PIS_API=2
  MOZ_PIS_MOZBINDIR="${dist_bin}"
  MOZ_PIS_SESSION_PID="$$"
  MOZ_PIS_USER_DIR="${MOZ_USER_DIR}"
  export MOZ_PIS_API MOZ_PIS_MOZBINDIR MOZ_PIS_SESSION_PID MOZ_PIS_USER_DIR
  
  case "${1}" in
    "start")
      for curr_pis in "${dist_bin}/init.d"/S* 
"${HOME}/${MOZ_USER_DIR}/init.d"/S* ; do
        if [ -x "${curr_pis}" ] ; then
          case "${curr_pis}" in
            *.sh) .  "${curr_pis}"         ;;
            *)       "${curr_pis}" "start" ;;
          esac
        fi
      done
      ;;
    "stop")
      for curr_pis in "${HOME}/${MOZ_USER_DIR}/init.d"/K* 
"${dist_bin}/init.d"/K* ; do
        if [ -x "${curr_pis}" ] ; then
          case "${curr_pis}" in
            *.sh) . "${curr_pis}"        ;;
            *)      "${curr_pis}" "stop" ;;
          esac
        fi
      done
      ;;
    *)
      echo 1>&2 "$0: Internal error in moz_pis_startstop_scripts."
      exit 1
      ;;
  esac
}

#uncomment for debugging
#set -x

moz_libdir=/usr/local/lib/firefox-0.8.0+
MRE_HOME=/usr/local/lib/mre/mre-0.8.0+

# Use run-mozilla.sh in the current dir if it exists
# If not, then start resolving symlinks until we find run-mozilla.sh
found=0
progname="$0"
curdir=`dirname "$progname"`
progbase=`basename "$progname"`
run_moz="$curdir/run-mozilla.sh"
if test -x "$run_moz"; then
  dist_bin="$curdir"
  found=1
else
  here=`/bin/pwd`
  while [ -h "$progname" ]; do
    bn=`basename "$progname"`
    cd `dirname "$progname"`
    progname=`/bin/ls -l "$bn" | sed -e 's/^.* -> //' `
    if [ ! -x "$progname" ]; then
      break
    fi
    curdir=`dirname "$progname"`
    run_moz="$curdir/run-mozilla.sh"
    if [ -x "$run_moz" ]; then
      cd "$curdir"
      dist_bin=`pwd`
      found=1
      break
    fi
  done
  cd "$here"
fi
if [ $found = 0 ]; then
  # Check default compile-time libdir
  if [ -x "$moz_libdir/run-mozilla.sh" ]; then
    dist_bin="$moz_libdir"
  else 
    echo "Cannot find mozilla runtime directory. Exiting."
    exit 1
  fi
fi

script_args=""
moreargs=""
debugging=0
MOZILLA_BIN="${progbase}-bin"

# The following is to check for a currently running instance.
# This is taken almost verbatim from the Mozilla RPM package's launch script.
MOZ_CLIENT_PROGRAM="$dist_bin/mozilla-xremote-client"
check_running() {
    "${run_moz}" "$MOZ_CLIENT_PROGRAM" -a "${progbase}" 'ping()' 2>/dev/null 
>/dev/null
    RETURN_VAL=$?
    if [ $RETURN_VAL -eq 0 ]; then
        echo 1
        return 1
    else
        echo 0
        return 0
    fi
}

if [ "$OSTYPE" = "beos" ]; then
  mimeset -F "$MOZILLA_BIN"
fi

ALREADY_RUNNING=`check_running`

################################################################ Parse Arguments
# If there's a command line argument but it doesn't begin with a -
# it's probably a url.  Try to send it to a running instance.
_USE_EXIST=0
_NEW_WINDOW=
_optOne="$1"
case "${_optOne}" in
        -*) 
                ;;
        *)
                _USE_EXIST=1
                ;;
esac

_optOthers=
_optLast=
for i in "$@"; do 
        _optLast="${i}"
done #last arg

for i in "$@"; do
        [ $i = ${_optLast} ] && break
        _optOthers="${_optOthers} ${i}"
done #others arg

#???: needs check if othersopt begin with -* ?
if [ `expr "${_optLast}" : '.*:/.*'` -eq 0 -a \( -f "${_optLast}" -o -d 
"${_optLast}" \) ]; then
        # Last argument seems to be a local file/directory
        # Check, if it is absolutely specified (ie. /home/foo/file vs. ./file)
        # If it is just "relatively" (./file) specified, make it absolutely
        [ `expr "${_optLast}" : '/.*'` -eq 0 ] && 
_optLast="file://`pwd`/${_optLast}"
elif [ `expr "${_optLast}" : '.*:/.*'` -gt 0 -o -n "${_optOthers}" ]; then 
#???? like before...
        _NEW_WINDOW=1
fi
################################################################ Parse Arguments

########################################################################### Main
if [ $ALREADY_RUNNING -eq 1 ]; then
        # There's an instance already running. Use it.
        # Any command line args passed in?
        if [ $# -gt 0 ]; then
                # There were "some" command line args.
                if [ ${_USE_EXIST} -eq 1 ]; then
                        # We should use an existing instance, as 
_USE_EXIST=$_USE_EXIST=-1
                        _open_type="window"
                        #_open_type="tab"
                        _remote_cmd="openURL(${_optLast} , new-${_open_type})"
                        "${run_moz}" "$MOZ_CLIENT_PROGRAM" -a "${progbase}" 
"${_remote_cmd}"
                        unset _remote_cmd _open_type
                        exit $?
                fi
        else
                # No command line args. Open new window/tab
                #exec "${run_moz}" "$MOZ_CLIENT_PROGRAM" -a "${progbase}" 
"xfeDoCommand(openBrowser)"
                "${run_moz}" "$MOZ_CLIENT_PROGRAM" -a "${progbase}" 
"xfeDoCommand(openBrowser)"
                exit $?
        fi
fi
# Default action - no running instance or _USE_EXIST (${_USE_EXIST}) ! -eq 1
########################################################################### Main

while [ $# -gt 0 ]
do
  case "$1" in
    -p | --pure | -pure)
      MOZILLA_BIN="${MOZILLA_BIN}.pure"
      shift
      ;;
    -g | --debug)
      script_args="$script_args -g"
      debugging=1
      shift
      ;;
    -d | --debugger)
      script_args="$script_args -d $2"
      shift 2
      ;;
    *)
      moreargs="$moreargs \"$1\""
      shift 1
      ;;
  esac
done

export MRE_HOME
eval "set -- $moreargs"

## Start addon scripts
moz_pis_startstop_scripts "start"

if [ $debugging = 1 ]
then
  echo $dist_bin/run-mozilla.sh $script_args $dist_bin/$MOZILLA_BIN "$@"
fi
"$dist_bin/run-mozilla.sh" $script_args "$dist_bin/$MOZILLA_BIN" "$@"
exitcode=$?

## Stop addon scripts
moz_pis_startstop_scripts "stop"

exit $exitcode
# EOF.

#!/bin/bash
tar xjf firefox-1.0.4-source.tar.bz2 &&
cd mozilla &&
rm -f mozconfig &&
cat > mozconfig << "EOF"
. $topsrcdir/browser/config/mozconfig
mk_add_options [EMAIL PROTECTED]@/firefox
ac_add_options --enable-default-toolkit=gtk2
ac_add_options --enable-xft
ac_add_options --disable-freetype2
ac_add_options --with-pthreads
ac_add_options --enable-optimize
ac_add_options --disable-tests
EOF
rm -rf firefox &&
mkdir firefox &&
make -f client.mk build &&
make -C firefox/browser/installer &&
tar xzf firefox/dist/firefox-1.0.4.en-US.linux-i686.tar.gz -C /usr/lib &&
ln -s ../lib/firefox/firefox /usr/bin/firefox &&
echo "Rejoice, 'tis done!"
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