Dear Piero,
The way the SWAN startup script works is by exporting new values for the variables you would like to set, for example:
export PYTHONPATH=/cvmfs/lhcb.cern.ch/lib/lhcb/GAUDI/GAUDI_v32r2/Gaudi/python:$PYTHONPATH
Do the commands you run inside your SWAN startup script do such kind of export?