Lossless chipping/crackling??

It might be that the amp isn't able to amp the ultrasones properly. It's also possible the album you downloaded suffered the same fate as many albums these days do. What I mean by that is that it was mastered too hot. Meaning too loud. Here is a video of what might sound like:

http://www.youtube.com/watch?v=3Gmex_4hreQ&feature=related

Clipping can (and does) still occur on lossless files if you try to get past the 0 dB limit. This can be caused by intersample peaks or just regular horrible mastering.

To try and figure out what the problem is I would try to get a few more lossless files and try those. Maybe rip those yourself from CDs you own. 

Edit: You might also have an EQ on or some other DSP which is making everything clip. I'd check for that as well.

On the iPhone, ideally, take the signal via LOD to your headphone amp.  That would remove any contribution from the iPhone's analog section. 

From the Vaio, are you taking the signal directly from the headphone out?  Check your sound settings and make sure you have all process/effects turned off. 

I gather that you can optimize a number of settings in Windows and there is also a choice of music player software you can try.  To get a taste, take a look here http://www.usbdacs.com/Windows/Windows.html.  While part of this describes the setup for an external dac, I think taking a look at some of the settings may help.

"Obtaining lossless files online" - what exactly does that mean?

If you're buying tracks from HDTracks.com it's one thing.  Downloading from unknown torrents is an entirely different thing.  For all you know, you could be listening to mp3s converted to FLAC.

All of the other suggestions for checking are good as well.

Oh, and yes, MJ's albums sound pretty good.  But only owning Thriller on vinyl, I can't say how his albums are mastered.  The Number Ones album, however, is clipped to hell just like most other albums today.  It does manage to sound fairly good still, and I honestly don't think I would never have heard this myself, but look at this:

That's absolutely massive clipping on Billie Jean.

Like I said, while I know the album clips and is fairly compressed, it still sounds much better than, say, What's the Story (Morning Glory) by Oasis or the new "Smashing Pumpkins" album Zeitgeist, which are among the worst mastered recordings yet.  (I put "Smashing Pumpkins" in quotes since the reformation is really a shadow of the former band...)

In fact, I think it still sounds pretty good.  Of course, I'd like to see it without the clipping.  If I compared the version on Number Ones directly with a non-clipping master (I assume the original CD master was good), I may well be able to easily hear the the clipping and compression.

But anyway, my point is that the artifacts you're hearing could also be a result of the compression of an album.

i also have little crackling on my sound. Always at the same moment on a song whether it is mp3 or flac. It is on all my headphones and every gain. (see profile)

so, it's on every source (laptop, desk computer, mp3 player), with or without dac, whatever the amp, or the heaphones. So it must be the file is like corrupted or something. It really is bothering i loose a lot of pleasure listening to music like this. Every music file i have is downloaded (legally of course ). Maybe i have a bad internet connection...

I get the odd album that clips, regardless of format or bit rate, and it is always on newer albums or sometimes on older stuff that has been remastered.  As a previous poster mentioned, it is usually because it was recorded and mastered waaaaay to loud.  Anyway, I've been using mp3gain for a couple years now, does a bang up job of fixing all that clipping.  Takes a couple minutes with this software to fix, which for me is better than trying to find a version that does not clip.

I still haven't found a solution to my problem. It's really unlistenable :/ To describe more precisely there are "tiny clicky sounds" or "very small clipping"

If i download a song (for exemple barry lyndon- sarabande) whether it's mp3 320, flac, ogg, the clicks remains the same, at the same position. It happens on youtube also...

If the tracks were mastered this way then you're outta luck. Small amounts of clipping can be inaudible on speakers (in the studio) but with headphones you can clearly hear it. Yes, it's annoying but that's the way it is.

Youtube is another matter, because it re-compresses (transcodes) music and therefore ruins sound quality depending on the bitrate and previous format.

In the best case it's just some single, very short *click* sounds, in the worst it sounds like crackling. (Post)processing the files could probably "fix" most of that but I don't know if you want to do that and have the tools (many DAWs have some restoration tools built-in).

If the problem are mp3's that clip you could try to scan them with ReplayGain and apply the gain to the mp3 data (with foobar2000 for example) if you're listening on a portable player that doesn't support ReplayGain.