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.

It has to be converted to standard PCM format which is was format before it can be converted to analog.  So there is an extra step in the process.   If done properly it should not matter but may not be in some cases.  But the information content of the source is the same assuming the software that encodes the flac does its job correctly.  

So Flac may not sound as good in some cases or vice versa but if so its not because of the format.   Just like how different cartridges may sound better or worse playing the same record.  
Computer decompresses data, places it in the memory and adds timing to create and output S/Pdif (PCM). The only difference, assuming bit perfect conversion, can be jittery S/Pdif timing, that would add noise to music but dynamic range should be the same. Since computer timing errors would be very small noise would be added to mid and high frequencies. I cannot imagine how it could affect the bass.
Just as you assume flac is indeed lossless, I think it is fair to assume that the decompression algorithm on any reasonable player does its job correctly.

Have you tried zero compression flac? It is not compressed but has a flac header?

Systems that play from memory can decompress a flac file and then put the PCM into memory for playing. At that point, the computing to decompress is not important. Have you tried that approach?
DTC, the short answer to your questions is no.

The longer answer is as follows. The FLAC file(s) I am speaking of are "created" outside of my control. Specifically, I download them from bt.etreeg.org using Utorrent (64-bit). I then burn to CD using Ashampoo version 6. Playback via Emotiva ERC-3, Musical Fidelity M6si, Golden Ear Triton One's. It as at that point in some instances (music passages) I can notice more "bass energy" (simplistic term but that will suffice for now). Then, I have compared that point (time and track data) in order to play back the FLAC and decompressed WAV version of it via my computer, Gateway NV79. That connects to my M6si via USB. Granted, the DAC on the M6si differs from the DAC in the ERC-3, however, that should have nothing to do with this because what I am finding is that the WAV when played back is more representative (all around but looking at the bass energy here) to the ERC-3 playback than the FLAC. This is to say the FLAC and WAV when played via the same computer and at the same track and time index produce different (in some passages that I can detect using my ears only) bass energy. Also, I would be remiss if I didn't point out that I use VLC player (latest version) and the "settings" are kept the same when playing.
The comparison between using the ERC-3 or the PC as a transport  is, of course, not a good way to make the comparison. It sounds like you also compare the FLAC and WAV both played back from the same computer and using the same equipment. That is a valid comparison. If you are doing that, then you should be able to convert the flac to flac with zero compression as a test. You might also want to try a couple of different players, to verify that it is not some issue with the player.

This issue has been discussed hundreds of times. Some people say they hear a difference, most say they do not. If you near a difference, it is more likely to be an issue with your player or the PC than with just the format. That is one reason I suggested zero compression. It might also be interesting to try different compression levels, like 1,2,3 up to whatever you are currently using.