Too Many Apps Resuming on Startup

Hey so I'm having an issue that's seriously driving me crazy. Here are the symptoms:
-When I restart or shut down/turn on my computer, way too many apps are opening. Like I quit some apps, continue using my computer, eventually restart it, and the apps I quit re-open, even though they were not running when Lion shut down.
NOTE: This happens even if I uncheck "Re-open windows when logging back in"!! It still opens up all my apps again!
-When I do things in apps like sticky notes such as creating new notes/editing existing notes and then quit the application, it opens from the state it started at (all new notes dissapear, edited notes revert).
-I open apps such as minecraft, and it loses all it's saved data and reverts me to a save I made like a week ago, but all future saves are gone.
-In system preferences, if I uncheck "restore windows when quitting and re-opening apps", then exit out of system prefs, when I open it back up it's checked again.
-I also tried turning Number of Recent Items: Applications to "Never" and when I restarted this was back to 10.
My Computer:
Macbook Pro (May 2011)
i5 Processor
8GB Ram
OSX Lion (latest version)
Does anyone know what's going on?
Thanks,
Emory

This is what disk utility said in the repair dialog box:
Repairing permissions for “Macintosh HD”
Group differs on “Library/Java”; should be 0; group is 80.
Permissions differ on “Library/Java”; should be drwxr-xr-x ; they are drwxrwxr-x .
Repaired “Library/Java”
Permissions differ on “System/Library/User Template/cs.lproj/Pictures/iChat Icons”; should be lrwxrwxrwx ; they are lrwxr-xr-x .
Repaired “System/Library/User Template/cs.lproj/Pictures/iChat Icons”
Permissions differ on “System/Library/User Template/hu.lproj/Pictures/iChat Icons”; should be lrwxrwxrwx ; they are lrwxr-xr-x .
Repaired “System/Library/User Template/hu.lproj/Pictures/iChat Icons”
Permissions differ on “System/Library/User Template/tr.lproj/Pictures/iChat Icons”; should be lrwxrwxrwx ; they are lrwxr-xr-x .
Repaired “System/Library/User Template/tr.lproj/Pictures/iChat Icons”
Permissions differ on “usr/share/devicemgr/frontend/admin/zh_TW.lproj/app/javascript.js”; should be lrwxrwxrwx ; they are lrwxr-xr-x .
Repaired “usr/share/devicemgr/frontend/admin/zh_TW.lproj/app/javascript.js”
Permissions differ on “usr/share/devicemgr/frontend/admin/zh_CN.lproj/app/javascript.js”; should be lrwxrwxrwx ; they are lrwxr-xr-x .
Repaired “usr/share/devicemgr/frontend/admin/zh_CN.lproj/app/javascript.js”
Permissions differ on “usr/share/devicemgr/frontend/admin/ru.lproj/app/javascript.js”; should be lrwxrwxrwx ; they are lrwxr-xr-x .
Repaired “usr/share/devicemgr/frontend/admin/ru.lproj/app/javascript.js”
Permissions differ on “usr/share/devicemgr/frontend/admin/ko.lproj/app/javascript.js”; should be lrwxrwxrwx ; they are lrwxr-xr-x .
Repaired “usr/share/devicemgr/frontend/admin/ko.lproj/app/javascript.js”
Permissions differ on “usr/share/devicemgr/frontend/admin/nl.lproj/app/javascript.js”; should be lrwxrwxrwx ; they are lrwxr-xr-x .
Repaired “usr/share/devicemgr/frontend/admin/nl.lproj/app/javascript.js”
Permissions differ on “usr/share/devicemgr/frontend/admin/it.lproj/app/javascript.js”; should be lrwxrwxrwx ; they are lrwxr-xr-x .
Repaired “usr/share/devicemgr/frontend/admin/it.lproj/app/javascript.js”
Permissions differ on “usr/share/devicemgr/frontend/admin/es.lproj/app/javascript.js”; should be lrwxrwxrwx ; they are lrwxr-xr-x .
Repaired “usr/share/devicemgr/frontend/admin/es.lproj/app/javascript.js”
Permissions differ on “usr/share/devicemgr/frontend/admin/fr.lproj/app/javascript.js”; should be lrwxrwxrwx ; they are lrwxr-xr-x .
Repaired “usr/share/devicemgr/frontend/admin/fr.lproj/app/javascript.js”
Permissions differ on “usr/share/devicemgr/frontend/admin/de.lproj/app/javascript.js”; should be lrwxrwxrwx ; they are lrwxr-xr-x .
Repaired “usr/share/devicemgr/frontend/admin/de.lproj/app/javascript.js”
Permissions differ on “usr/share/devicemgr/frontend/admin/ja.lproj/app/javascript.js”; should be lrwxrwxrwx ; they are lrwxr-xr-x .
Repaired “usr/share/devicemgr/frontend/admin/ja.lproj/app/javascript.js”
Group differs on “Library/Documentation/Applications/iTunes/Acknowledgements.rtf”; should be 0; group is 80.
Permissions differ on “Library/Documentation/Applications/iTunes/Acknowledgements.rtf”; should be -rw-r--r-- ; they are -rw-rw-r-- .
Repaired “Library/Documentation/Applications/iTunes/Acknowledgements.rtf”
Group differs on “Library/Documentation/iPod/Acknowledgements.rtf”; should be 0; group is 80.
Permissions differ on “Library/Documentation/iPod/Acknowledgements.rtf”; should be -rw-r--r-- ; they are -rw-rw-r-- .
Repaired “Library/Documentation/iPod/Acknowledgements.rtf”
User differs on “Applications/.DS_Store”; should be 0; user is 501.
Permissions differ on “Applications/.DS_Store”; should be -rw-rw-r-- ; they are -rw-r--r-- .
Repaired “Applications/.DS_Store”
Group differs on “Library/Preferences/com.apple.alf.plist”; should be 80; group is 0.
Repaired “Library/Preferences/com.apple.alf.plist”
The offending profile is still all screwed up.

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