Gnome, Fluxbox, and KDE have no control over or issue with the '-T' option.
Most distributions, if not all, configure their default shell (usually
bash) to step on the title of xterm windows.
I don't have the problem, presumably because the following appears in /etc/bash.bashrc:
# Commented out, don't overwrite xterm -T "title" -n "icontitle" by default.
# If this is an xterm set the title to [EMAIL PROTECTED]:dir
#case "$TERM" in
#xterm*|rxvt*)
# PROMPT_COMMAND='echo -ne "\033]0;[EMAIL PROTECTED]: ${PWD}\007"'
# ;;
#*)
# ;;
#esac
Perhaps something similar would take care of the OP's problem.
Patrick