Dock not showing at startup and the monitor keeps blinking

Hello,
I've had my macbook pro for about 2 years - it's a late 2011 model. I have all the latest updates installed and the latest operating system (10.9.2).
A couple of months ago I started having some issues with it - like one of the usb's not working (had to reset SMC) and mail suddenly marking mails as unread (this solved it: https://discussions.apple.com/message/24908508#24908508).
Now, for the second time, when I startup the laptop, the dock won't show and the monitor keeps blinking and the system is very slow. When it happened for the first time I decided to shut down the mac and waited some minutes before starting it up again. The problem didn't show up again. Now, a day later, the same thing is happening. Clearly this problem is not going away. Yesterday, after the problem I went and repaired the disc's permissions, hoping it was something caused by it.
Hoping someone here can help me with this issue, please.
Update:
So I managed to open finder and move a folder that I had previously downloaded away from the downloads folder (I read that tip from someone in a similar thread) and the dock showed up suddenly and the desktop stopped blinking.
Either way, that doesn't mean the problem won't show up again. So if anyway has any clues has to what should I be doing with my mac (do I need to rebbot it?), since lately I keep having a lot of issues with it...

Ok so now I have this problem pratically everytime I startup the laptop. I know I have to move some files around (it doesn't have to be in the downloads folder, now it happens in the desktop as well) for it to stop. But this is pretty anoying. I'm looking for a permanent solution ofr this problem. Can someone help me, please?

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