Have you actually looked at the permissions in your User Library?
You should be the owner of all your library files and have read/write priveleges for the files, and execute for the folders.
Listing the "Applications Support" folder in the Terminal with the following command should show something similar to this:
% ls -l ~/Library/Application\ Support
total 368
drwx------ 13 dreschle staff 442 Jun 2 04:07 AddressBook
drwxr-xr-x 27 dreschle staff 918 Nov 29 2011 Adobe
drwxr-xr-x 18 dreschle admin 612 Jun 1 07:47 Aperture
drwxr-xr-x 3 dreschle staff 102 May 21 2008 Aquamacs Emacs
drwxr-xr-x 3 dreschle staff 102 Jul 23 2009 ArcSoft
drwxr-xr-x 3 dreschle staff 102 May 6 2009 ArtRage 2
drwxr-xr-x 9 dreschle staff 306 Dec 30 17:45 Audio Hijack Pro
drwxr-xr-x 5 dreschle staff 170 May 9 00:47 Automator
drwxr-xr-x 9 dreschle staff 306 Feb 7 20:36 Backup
drwxr-xr-x 4 dreschle admin 136 Nov 13 2010 Bento
drwxr-xr-x 15 dreschle staff 510 Jan 22 10:41 BibDesk
....
the codes "xrwx" show that the item is a library (d) and the owner (columns 2,3,4) has write, read, and execute priveleges.
and listing the contents of the Application support folder:
% ls -l ~/Library/Application\ Support/Aperture
total 672
-rw-r--r-- 1 dreschle admin 165656 Feb 5 09:43 Adjustment Chain Presets.plist
drwxr-xr-x 13 dreschle admin 442 Mar 27 01:23 Adjustment Preset Brushing
-rw-r--r-- 1 dreschle admin 1111 Apr 6 16:10 AdjustmentPresets.plist
drwxr-xr-x 4 dreschle admin 136 May 26 10:04 Command Sets
-rw-r--r-- 1 dreschle admin 46072 May 5 16:00 Export Presets.plist
-rw-r--r-- 1 dreschle admin 2629 May 30 18:42 FileFolderPresets.plist
-rw-r--r-- 1 dreschle admin 4021 May 30 18:42 FileNamingPresets.plist
-rw-r--r-- 1 dreschle admin 1008 May 30 16:10 Import Presets.plist
-rw-r--r-- 1 dreschle admin 8218 Apr 9 06:49 Metadata Presets.plist
-rw-r--r-- 1 dreschle admin 28855 Jun 1 07:47 MetadataSets.plist
drwxr-xr-x 4 dreschle staff 136 Apr 28 13:59 Plug-Ins
-rw-r--r-- 1 dreschle admin 15020 Apr 29 19:17 PrintPresets.plist
-rw-r--r-- 1 dreschle admin 1107 Apr 6 16:10 Raw Decode Presets.plist
-rw-r--r-- 1 dreschle admin 24687 May 30 18:31 Slideshow Presets.plist
drwxr-xr-x 9 dreschle admin 306 Apr 15 23:27 WatermarkImages
-rw-r--r-- 1 dreschle admin 14453 Apr 13 19:43 Web Export Presets.plist
What are the priveleges in your user library? You are saying that the Aperture seting don't exist, but do the other folders on the path to ~/Library/Application\ Support/Aperture exist, and what are the protection codes (drwx) for the folders along the access path?