I have observed (heard and then tested so as to confirm) the following “condition” as it relates to the widely debated issue of FLAC quality. The purpose of this topic is to gather opinions as to whether or not your observations are similar too – and therefore support – my own.

It is widely understood and accepted that a FLAC file while “compressed” is “lossless” as compared to its corresponding WAV file. Let’s assume (i.e. not debate) this is completely true. What I am noticing is that when the FLAC file is “played” via any FLAC player it sounds different from the sound of the “same” (equivalent decompressed FLAC) WAV file when played back via the same player that was used to play the FLAC file. This is specifically noticeable (to me) in the low frequency spectrum. The WAV has considerably more “sonic energy” that manifests itself as appearing to be a bit louder, wider in frequency range and perhaps even dynamic range as compared to the FLAC equivalent.

I’m curious as to your findings when you compare a FLAC file played natively as compared to the WAV equivalent played via the same player (for example, play both the FLAC and WAV via VLC media player) or practical equivalent, such as if the FLAC was burned to CD and you are comparing the FLAC played via VLC and the CD played via a CD player.

I am further assuming that the WAV file is a more accurate representation of the audio than the FLAC. This is to say that should you agree with the aforementioned, it would be preferable to play the WAV file or decompress the FLAC file before using it.

There is no difference between flac and wav. If there is, then you need a better DAC.
thanks dtc. your response makes sense. perhaps at some point I may attempt to inspect the binary but I'm good for now. curious though as you indicate it can be a result of the way the program writes the data (padding zeros, etc.), do you observe any byte difference? 
I went through this exercise a few years ago and did notice byte differences. But when I did binary compares there was no difference. That is why I think you are just seeing padding differences.  At one point I looked at the files with a binary editor and that also convinced me that the files were the same, other than padding.

There were some "interesting" articles in Absolute Sound a while ago where 2 guys went back and forth between wav and flac multiple times and convinced themselves that the sound degraded the more times they did the conversions. It was a very controversial set of articles and, in the end, most people dismissed their "research", but  there are still people who seem to believe that even though the conversions are bit perfect  they can  change the sound. I've given up worrying about it
Thank you so much dtc for the confirmation as to the byte size question. You've convinced me and saved me some time in wanting to do the file binary compare. No need if you too have noticed a small difference.
FLAC is an audio encoding format. It’s also a very good one for a number of reasons. FLAC is a “lossless” format, meaning none of the data from the source recording is compressed or removed (assuming you use the same bit depth [not the same thing as bit rate] and frequency range). This is inarguably a good thing. Lossless is the word of the year (or last 3) among audiophiles (and those who like to consider themselves audiophiles), but the implications of lossless have been twisted and manipulated in ways that are just not factually supported.
Why is FLAC awesome (and is it awesome)? Really, it is – as much as I hate FLAC listening purists, FLAC has a real place in the digital audio world that should not be overlooked.
You know of one other lossless audio format called .WAV. Yep, that same, good ‘ol format that your Windows system sounds are encoded in (though that’s 8-bit and usually mono). WAV preserves 100% of audio information in 16-bit 44.1KHz stereo format when ripping audio from a CD. FLAC is better than WAV for two reasons. First, it does everything WAV does (lossless audio), but in a much smaller package (WAV is extremely inefficient in its use of space). Second, it allows the use of more tags (including “illegal” tags in Windows) for marking files. That’s it. Otherwise, same juice, different label. WAV does have the advantage of being more editing / DJ-friendly (also less work for the CPU since it’s hardware decoded), but that’s not really relevant to what we’re talking about here.This gets us to why FLAC is awesome. It’s all about preservation and archiving! FLAC uses less space than WAV, and allows more precise tagging, making it ideal as a long-term digital storage medium for audio. No matter how many times you copy it (well, in the relative sense), generation after generation, the source audio remains virtually unaltered. But WAV can be compressed for uploading http://www.videoconverterfactory.com/tips/compress-wav-file.html that is FLAC can not do well as WAV