I have a couple more ideas:
1. Try creating a new user (an Admin; I assume the user you are currently logging in as is an Admin). Make sure you have auto-login off, fix the permissions, reboot, and log in as the new user.
2. Maybe the "safe boot" isn't really safe. That is, maybe it does run non-Apple software. For example, if a third-party put plists in /System/Library/LaunchDaemons or /System/Library/LaunchAgents.
So it's worth doing
ls -l /System/Library/LaunchDaemons | grep -v com.apple
and
ls -l /System/Library/LaunchAgents | grep -v com.apple
and seeing what shows up. (I'm assuming "safe boot" loads them because they are in /System/Library, but I could be wrong.)
On my Mavericks system (which, again, does NOT have the problem), I see
$ ls -l /System/Library/LaunchDaemons | grep -v com.apple
total 16
-rw-r--r-- 1 root wheel 678 Sep 8 2013 bootps.plist
-rw-r--r-- 1 root wheel 672 Sep 8 2013 com.danga.memcached.plist
-rw-r--r-- 1 root wheel 574 Sep 8 2013 com.vix.cron.plist
-rw-r--r-- 1 root wheel 613 Sep 8 2013 exec.plist
-rw-r--r-- 1 root wheel 682 Sep 8 2013 finger.plist
-rw-r--r-- 1 root wheel 763 Sep 8 2013 ftp.plist
-rw-r--r-- 1 root wheel 246 Sep 8 2013 login.plist
-rw-r--r-- 1 root wheel 627 Sep 8 2013 ntalk.plist
-rw-r--r-- 1 root wheel 625 Sep 8 2013 org.apache.httpd.plist
-rw-r--r-- 1 root wheel 771 Sep 8 2013 org.cups.cups-lpd.plist
-rw-r--r-- 1 root wheel 1480 Sep 8 2013 org.cups.cupsd.plist
-rw-r--r-- 1 root wheel 489 Sep 8 2013 org.freeradius.radiusd.plist
-rw-r--r-- 1 root wheel 900 Sep 8 2013 org.isc.named.plist
-rw-r--r-- 1 root wheel 495 Sep 8 2013 org.net-snmp.snmpd.plist
-rw-r--r-- 1 root wheel 625 Sep 8 2013 org.ntp.ntpd.plist
-rw-r--r-- 1 root wheel 966 Sep 8 2013 org.openldap.slapd.plist
-rw-r--r-- 1 root wheel 585 Mar 23 2012 org.postfix.master.plist
-rw-r--r-- 1 root wheel 1284 Sep 8 2013 org.postgresql.postgres_alt.plist
-rw-r--r-- 1 root wheel 238 Sep 8 2013 shell.plist
-rw-r--r-- 1 root wheel 884 Sep 8 2013 ssh.plist
-rw-r--r-- 1 root wheel 260 Sep 8 2013 telnet.plist
-rw-r--r-- 1 root wheel 715 Sep 8 2013 tftp.plist
$ ls -l /System/Library/LaunchAgents | grep -v com.apple
total 8
-rw-r--r-- 1 root wheel 596 Sep 8 2013 org.openbsd.ssh-agent.plist
If you other items, maybe they are the problem.