Do you have to kill PHP processes with "SIGKILL" or just "SIGTERM"?
LSWS always try to stop all fcgi processes stated by itself with "SIGTERM" before it quits. So, unless LSWS lost tracking to PID of those processes, or those processes does not respond to "SIGTERM", those processes should be killed.
I guess for some reason lsws lost tracking to those PID.
I will take a closer look on this issue.