Permissions in Library

I've been having a few issues since I changed permissions in the Prefrences folder of my Library (in my account only). I think (but I'm not positive), some of the issues I've had in the last few weeks may be related. Before I did it, the program GarageBuy was telling me the preferences could not be read and quit when I tried launching it. If I went to its preferences, although I had read/write permissions, I had to set them again to read/write (visually, there was no change, but under the hood, something must have happened).By doing this, I could launch the program. However, the next time, I'd have to go through the same process.
My deduction was that there was something really off with the permissions and since preference files are not much more than text files, I thought it shouldn't be a big deal to change all permissions inside the Preferences folder. I therefore set my user to read/write on the Preferences folder and I applied the change to all subfolders.
Since my change leads to my user having read/write permissions in the whole folder I thought it could not be a bad thing.
One of the issues I have, that may be related, is that Time Machine does not work at all anymore.
It does not seem to find system files. Here's an example of message I have in the console:
com.apple.backupd[917]: 2009-01-03 18:38:16.179 FindSystemFiles[918:713] FSOpenIterator failed
Backup does not seem to be able to save its preferences either. I can set a destination drive and a backup time but when I quit, it forgets everything.
I've repaired permissions lots of times, repaired disks too, reinstalled a combo 10.5.6 and repaired again. All to no avail. Any idea why this is happening and how I can solve this?
(I have seperate threads for my issues with TM and Backup but with no solutions so far)

you should already be the owner of everything in your home directory. if you are not then your home directory permissions are more messed up than I thought. you should reset them all. However, this should have no bearing on TM which is set up on a system wide level. TM doesn't care at all about permissions on your home directory. I have no idea what GarageBuy is but it and Backup might be affected by bad permissions on your home directory.
to reset the permissions and ACLs on the home directory follow the instructions in this kb article:
http://support.apple.com/kb/TS1334?viewlocale=en_US
after you are done with that log in normally and run
sudo chown -R `id -un`:`id -gn` ~
this will make you the owner of everything in your home directory which is how it should be. Please do not change the command and do not restrict it to any subfolders.

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