MacBook Pro 2012 - Lagging and slow boot-up I've left my Macbook pro to sleep with a lot of programs and memory used (probably lot of swap used as well)

And when I've waken it up, it started to have 60 s lags then 5-10 seconds of responsiveness and again 60s lag (with death beach ball)

When I boot up it takes 30 seconds and around 120 seconds to login. (Earlier it was like 20 s for everything) 

The craziest part is that when I turn on the Black magic benchmark test of the hard disk drive - I have Samsung 840 evo with 250GB - it goes without lag... System is not so fast but it goes on without lag.

When o boot to Windows it  lags as well (almost without time for responsiveness)

Is this disk problem ? 

The video show it all (skip too the moments when something is changing)

Laging Mac OS X with SSD disk Samsung 840 evo: http://youtu.be/9a7CjKuzzsw

Thank you very much in advance.

EDIT:

Interesting info: I've erased this disk, installed via USB SATA connector the Mac os x 10.9.

Then booted. From USB, NO PROBLEM!

Then mounted it to the SATA connector in the Macbook itself. And the same problem ... Of 5 minutes boot up time and extremely laggy Mac.

Maybe the problem is in the firmware of Mac itself ?
disk seems fine, as your tests indicate.
first, best chance:

have you done a safeboot to clear out some caches and repair the hard drive?
shift key down at boot up.  then when it comes up, do a regular reboot.