TextEdit, Calca, Numbers photos syncing stop to work

Hello,
Since Mavericks have been having some obscure, difficult to formulate problem. In the nutshell, some programs (TextEdit, Calca to name the few) cease to work under unknown circumstances (nothing magical, I just missed the moment when it happens).
A couple of times photos synchronization (with iOS devices using iTunes) stopped to work. Synchronizing them took so much time that I never had patience to wait till it ends (waited an hour or more). Guess it somehow may be connected to the former problem.
I have the strong inkling that it happens after some new app is installed. When I installed Team Viewer a month ago or so the photo sync stopped to work also. After rebooting everything returned to normal.
Week ago installed Aquamacs, sync wasn't affected, however TextEdit was.
After restarting the system everything returns to normal.
How TextEdit doesn't work (the same applies to other programs):
Icon of the App jumps for a while. Menu of the App appears. No windows of TextEdit, menu irresponsive. Terminating only by 'Force Quit'. See no relevant records in the log (Console). If the records in log somehow connected to the TextEdit, the relation is too distant for me to recognize it.
Checked the disk with Disk Utility, nothing serious,
"The volume Macintosh HD appears to be OK.",
some messages of permissions like
"Permissions differ on “Applications/Safari.app/Contents/Resources/Safari.help/Contents/Resources/"
Googling and analyzing for some months. Many quite contradicting suggestions, like reinstalling the OS or just checking the /Library permissions. None of them looked to me very reliable to rush doing it specially killing the OS.
Seems the bug (?) affects the app which uses iCloud.
Presently:
Mac OS X 10.9.2
MacBook Pro 13'
Careful usage, no suspicious software, mainly Apple made, except few like Aquamacs, VLC, TextMate, etc.
TextEdit Version 1.9 (310)

VladimirSch
One by one or a few at a time the permssions conflicts may not matter. Mine were quite large in number having accumulated over 4 OSX upgrades. There was also a problem with a "pointers / blocks" reference.
In my case the situtation led to a condition that manifest itself as if it were running out of disk space in a partition while Get-Info reported there was plenty of space unused. In adition some of the apps became quite slow and displayed erratically.
There may have been some other aspect as when the "Genius Bar" guy booted up my MBP with his network version of Mavericks he then ran a special version of Dick Utility that "fixed" the disk in about 1/2 hour wall clock.
I'm glad I live close to an Apple store.

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