after some more modifications to the mathematica frontend startup script
a workaround emerged: comment out the block which runs the "gltest"
executable:

# Check for GL and GLU version
#GLTest="env LD_LIBRARY_PATH=${M_LIBRARY_PATH} SHLIB_PATH=${M_LIBRARY_PATH} 
LIBPATH=${M_LIBRARY_PATH} 
${TopDirectory}/SystemFiles/FrontEnd/Binaries/${SystemID}/gltest"
#GLTestResult=`${GLTest} 1 1 1 2 ${userDisplay}  2> /dev/null | grep 
"GLTest_OK"`
#if [ -z "${GLTestResult}" ]; then
#       mesa="-mesa"
#fi

it seems that this executable crashes the xserver upon exit, most
probably since the "fatal io error 11" leaves the gl subsystem in a
strange state. it is hilarious that the test program can wreck such a
havoc...

i have also run this gltest executable with the gdb in batch mode but,
except for the exit status, there is no other noise reported. so this is
still a libgl bug, where some malformed call leaves it in undefined
state.

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https://bugs.launchpad.net/bugs/1256561

Title:
  starting mathematica 9 crashes xserver

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