Need help with problematic Macbook Pro Retina.

[Intelligent]

I used to only have to shut down my computer every month or so but now I have a worse problem.

Whenever i start my computer, everything works fine. Programs dont lag, everything is copied quickly, no high fan, no unusually high memory usage and extremly smooth performance. But after a few hours, 2-5 my I can't save anything. When i press save and choose the file name or when i click "Open File" in the menu bar the application freezes. Then i have to force quit it, and then i can't open it again. Then the same happens to every application, they all freeze and I can't do anything so I have to force quit them but then i can't open them again. Whenever i shut down my computer, it just freezes. So I always have to force shut the computer down. What is my problem?

I have repair my disk
I have repaired permissions
I have Reset NVRAM
I have Reset SMC
I have Deleted all Cache.

 

[TheIguana]

Is your drive FileVault 2 encrypted? I've had issues with lag on multiple Mac's now since the Yosemite update due to corrupted FileVault 2 partitions.

If your drive is FileVault encrypted, when you ran "Disk Repair," did you remember to click the partition listed as a dependant to your SSD and unlock it while in OS X's recovery mode?