Segmentation faults are often by hardware problems, e.g. RAM problems. I know many ispconfig 3 isntallations on lenny and none of it has segmentation faults and ther are already more thne 10.000 installations of ispconfig 3 so it might be that this is just related to your system od the bug in php is just triggered on your system.
ISPConfig is transaction based and ispconfig will redo a transaction if the script diesd during processing.
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