pfSense

You are sure to be on latest version.
I recall this happened during package improvements and i fixed this regression by then.

Yeah I thought it was, but it happens on the newest snapshot.

I investigated this and i cannot see in any place in pfSense base code something like that being done apart
the sections mentioned here.

07:52 < eri--> hmm i do not see anywhere a rm or unlink being done on /usr/local/etc/rc.d
07:54 < eri--> ../../etc/phpshellsessions/removepkgconfig:7:echo "Removing startup files from /usr/local/etc/rc.d/...\n";
07:54 < eri--> ../../etc/phpshellsessions/removepkgconfig:8:exec("rm /usr/local/etc/rc.d/*");
07:54 < eri--> this is a phpshellsession
07:57 < eri--> and the new installer upgrade function seems to do the offending line
07:57 < eri--> ../../usr/sbin/pc-sysinstall/backend/functions-upgrade.sh:76:  rm -rf ${FSMNT}/etc/rc.d >/dev/null 2>/dev/null

Possibly the system log can help here since i cannot reproduce here.

1. echo test >/etc/rc.d/test
2. chmod 555 /etc/rc.d/test
   Install iperf package: /etc/rc.d/test is still there.
   Reinstall iperf package: /etc/rc.d/test is still there.
   Do you recall which package behaved like you describe?

it was actually fixed a while back, I just missed the fact the file was still there, it's not an issue