How to fix icons missing?

Hi
I have MacBook Pro Retina 15 with 16 GB RAM.
And I did stupid thing, I just turn off the swap file and using for a day my laptop. On the next day when I open my macbook, navigation icons in safari, finder, and in others apps, just dissapear. (system icons, like +/- and arrows, in finder all lest side dissapear and many others)
Then I turn on swap file back, and restart. But is't not helpd.
I tried just reinstall system and it helpd for half of day.
I tried to restore permissions, for account and fully.
I tried reset the VRAM.
I tried to reboot in verbose mode
I tried some more things
And one more interesting thing, I checked Keychain and it has alot duplicates of my login.
Please help me to fix it.
I created the another one user and it's ok, but when I login in to previous it still without icons.
But I want fix old one, because it has alot of custom things.
Many thanks!

Boot up holding command-r keys into your Recovery Volume.
The screen should give you these choices...
Restore from TM backup
Reinstall Mac OS X
Get help online
Disk Utility
First run Disk Utility Repair Disk, if you get errors run until no errors reported or reports "the disk cannot be fixed". Then, choose Reinstall OS X. This will be an install "in place" and shouldn't effect any of your own data or settings.
Be sure you have or make a good backup or make one.
EDIT: Oh wait... the other user is okay. I can't understand how missing swap files would effect only your own user.
Did you delete from private/var/vm?

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