MacOS – Strange Clipboard behaviour on OS X El Capitan

I've been experiencing a very weird clipboard behaviour on my mac.

This is my OS

I'm a developer and every now and then I need to copy paste code, text or even files around.

What I've been experiencing lately is that the clipboard is not being shared among applications.

For example I can't copy a url from Chrome and paste it into Safari. It doesn't give me any error, it just wont paste anything.

For example I just selected this page URL, but on the clipboard I see the URL dropbox added to my clipboard.

Another strange issue is that I use Sublime Text on a day to day basis, and sometimes if I need to copy and paste code somewhere else, it either wont paste anything at all or adds sometimes 10 new lines between each line of what I copied and sometimes 1000s of new lines in between. Which is very annoying.

I've tried restarting the clipboard from the terminal and from Activity Monitor and still the same issue.

Sometimes when I quit and reopen sublime, the issue in sublime itself gets fixed but for a short period of time. It then comes back.

I also use Alfred 2 for workflows and shortcuts which has a clipboard history, but when it starts happening it wont copy into it's clipboard either.

Sometimes copying and pasting works just with the mouse and sometimes not even with it.

I've also tried repairing permissions, run Onyx and repair everything.

UPDATE
I recently tried rebooting in Recovery mode to repair permissions as well as clearing the NVRAM but I'm still experiencing the same thing.

So far the only solution I have found is a reboot, which makes it work for a while.

Any clues?