I've had an idea about this but don't know if it is feasible or how to construct the command.
Currently the TightVNC server is started via bootlocal.sh using display number 9. As outlined in the tightvnc.tcz info file the server desktop is subsequently configured using
DISPLAY=:9 jwm &
etc... issued from a file in ~/.X.d
Is it possible to use the same method to create a variable that will switch off transparency, for a terminal opened in display number 9, via the JWM "Start" menu?
If so, what would be the command use?