At this point I thinking a typical fix solution has been further complicated by user tampering with system and hidden files.
So I'm going to recommend you do this.
1: Backup your users files folders (music, pictures, movies, documents, etc) to a regular external drive in addition to any other backups, like bootable clones/TimeMachine and disconnect all drives from the machine.
Emergency backup procedure
Drag and drop copy your users file folders (music, pictures, documents etc) to a regular external powered drive as soon as possible.
Do not use, setup or trust only TimeMachine at this troubled time as it will copy corrupted data and we need just your users files safe just in case. TimeMachine cannot be used with a Windows PC.
Unmount and Disconnect all external drives once the backup process is completed.
If you have any over 4GB sized files, those won't copy to a standard formatted FAT32/MSDOS drive from the factory, if you need to save these 4GB+ files use another blank/empty drive and use Disk Utility to format it 1 Partition, Option: GUID, Format: OS X Extended Journaled (the standard default)
Mac's cannot copy to nor format a NTFS drive. exFAT format to be used with a Windows machine must be right click formatted by Windows, not OS X (does it wrong) XP macines can install a free exFAT update from Microsoft. Vista-Win 8 can format exFAT. OS X 10.6.5 and up can use exFAT.
Formatting a drive will erase all data on it, so make sure there is nothing you want remaining on the drive.
2: Next proceed with fixing your machine in the Steps here in order to catch other issues and your original problem.
To fix the changes in your ~/Library, your going to have to transfer a copy of your users files folders (music, pictures, movies, documents etc, no Library) into a new account on the machine via the Shared folder, then log into the new account and delete the old one, reboot and recreate the same account again, then transfer files back and do a #6 Repair Users Permisisons to reset those file permisisons to the new account (even if it has the same name)
Don't forget to export bookmarks, emaill addresses, addressbook contacts and other things.
See Step #17 and this User Tip
What this will do is give you a brand new ~/Library and all your problems should be resolved hopefully.