has anybody else noticed this about flac audio?

Regarding the difference in sound between vinyl and digital, what you are really hearing is a whole constellation of differences between your turntable and your digital player/converter. To start with it is highly likely that there is a frequency response difference between your cartridge and your digital gear. Cartridges are notoriously not flat in frequency response. This alone could explain what you are hearing. I've never encountered your theory (second vs. third soundstage) in all my years of geeking out on such things. In my own case my vinyl rig sounds remarkably similar to my digital rig with excellent imaging in both formats.

I'm about 2/3 through ripping my 4000+ CD collection. I decided at the outset to use dbPoweramp with no compression. Hard drive space is cheap and I wanted to make life as easy as possible on my digital gear. I did this even though I ripped a couple of CDs at different compression levels to see if I could hear the difference between compression level 5 and no compression. I couldn't hear any difference (files played through Foobar on i7 laptop, Windows 7, USB cable, PS Audio PerfectWave Mk II DAC, Krell pre and amp, Thiel CS6 speakers).

IMO what you are hearing on your system is unusual and bears further investigation. I think it's likely that different gear, including your computer, would alter this situation. FWIW I don't agree with your theories of why this is happening but I don't doubt that you hear what you claim.

This is my first post guys, but I found this discussion interesting, and compelling on a few levels, so had to chime in.I believe it's clearly a fact that a digital file will sound different than it's vinyl counterpart. There are so many variables involved, with the playback equipment being only one of the reasons for the music to sound different.I have a few hi res digital albums that I also own on vinyl. I obtain the digital files from places like HDTracks and Quobuz, and I trust that they are obtaining them from sources that take care in the quality of the product. These all sound (to me) very good. But not the same as their vinyl counterpart. It's pretty easy to A-B these for very close listening. I don't have "top of the line" equipment, but consider it "very good" equipment. But I would have to think there's more to the differences than just the playback path, as the source creation paths are very different as well.I have master files of my niece's (a recording artist) latest album destined for CD release. These were sent to me via internet by my brother. They now reside on my music server, and I play them back via  a Pro-ject DS2 T via a Jolida Glass FX Tube DAC. I burned a cd using these files and play them on my Oppo BDP-83SE. These sound very slightly different to me, even though they came from the same source at the same resolution (32/88.2k). In this case, it has to be the playback path since that's the only difference.I'm currently looking for a phono preamp that I can use to transfer some of my vinyl collection to digital at high resolution. It'll be interesting to see (hear) how resulting files compare with the vinyl sources in this very closely controlled environment.

Just a comment to point out that there is a BIG difference between comparing a LP against the commercial CD or hi-rez release versus comparing the LP against a digital copy of the LP made using your own equipment.

Anyone who has ever looked into what it takes to make a LP will understand why vinyl playback can be so unique. First, the RIAA curve used when cutting the LP has a 40 dB swing from bass to treble. This curve must be matched exactly on an inverse mirror image basis for playback. Second, phono cartridges are a mechanical device that have just as much variability as speakers. When was the last time anyone thought two different brands of speakers sounded identical? Add to that the unique technical constraints involved in cutting an LP and the trade-offs involved (time on each side versus amplitude, groove variability, etc.) and it is no wonder that LPs offer such fertile ground for searching out a unique sound.

Digital recording certainly has its own unique considerations, but they are on a completely different plane. Given that, it is no surprise that the LP release almost never sounds the same as the commercial CD or digital download.

However, when I make my own digital copy of an LP, using my own equipment, I find the digital version is very difficult to distinguish from the vinyl. The digital version has done an excellent job of capturing the quirks and traits of the LP, so much so that I cannot reliably tell the difference between the two versions if I have been careful in my transfer (no clipping, etc.) As noted earlier, I spent about ten years transferring over 1,000 LPs to digital and was so consistenly pleased with the results that I gave away most of that collection several years ago. I still don't miss having the vinyl. Nowadays, my turntable sits on a top shelf, unused, except for the rare occasion when I bring it out to transfer a LP for a friend or something unique that I've stumbled across.

mlsstl, can you describe your process and the equipment you are using? What resolution, sampling rates?

My conversion project started in the early 2000s and was finished eight or nine years ago. My equipment wasn't all that fancy - a Dual turntable with an Ortofon cartridge, and a Conrad Johnson preamp that fed a Dell PC with an aftermarket sound card (Creative Tech, as I recall.) Software used was Adobe Audition with recordings saved to flac file format at CD rates (16/44.1KHz.) 

Just a side note. I do not consider myself an "audiophile" -- the term has acquired way too much pretense over the years for me. I am just a music lover who also enjoys quality sound. I'm only describing what works for me. As they say, take what you want and leave the rest.