It may have lower quality than an entirely different source, but not as a result of the conversion to FLAC. What is in the FLAC is what is on the CD.
The volume difference may be accounted for if you set it to analyze for ReplayGain data on rip and then use ReplayGain on playback, but that's an adjustment that is made at playback, not during the ripping. The data in the FLAC is lossless as compared to the CD you gave it. It's not possible for it to be anything else. Audio information is not touched in the conversion to FLAC.
Wow. You really assume a lot don't you? Are you reading my post? I have already stated I am comparing quality, not volume. I have already stated My source is a commercial CD, made within the last two years. It is likely using the same source recording as the other versions of the song available on the internet and those other versions are of an inherently LESSER quality than the CD (or traditional FLAC files). As for your assumptions: your first statement is only true if the conversion worked as intended. That is my point. Chances are, It DIDN'T. (Unless I really did get a bum CD... how many faulty CD's make it to market?). It could be settings, it could be an issue with this particular flac encoder. I don't need you to tell me how FLAC works. I need to look for potential reasons as to why it didn't work.
EDIT: Your last statement about FLAC is also completely untrue. The Audio information is read from the CD. It then travels along a SATA cable into an I/O port. It then is sent into memory where MusicBee reads it in. The audio information is then converted into FLAC Format by the encoder which then compresses it (if compression is enabled). The final format is not identical to the original; otherwise we would have FLAC cd's. So yes... it is touched SEVERAL times and at any one of those points, something CAN go wrong.
Can you inform us of the exact CD? Artist, album, songs in question, a CD that is directly commercial from the publisher or one that is put out by a third party website? I guess what I'm asking is do you have a website for exactly where you purchased the CD from? Also, what kHz are the songs downloaded at? This can cause issues on certain systems.
FLAC is a lossless, compressed format. While it won't be exactly what the original source is on a bit-by-bit basis when looked at uncompressed, uncompressing it for playback will result in the same exact bit-by-bit quality song as the source. If this is not the case, then it is definitely something else causing the issue that we need to identify.
My bet is that the drive your are ripping the CD from isn't calibrated properly, the CD isn't properly ripped, replay gain is causing clipping, or you are comparing the songs to Youtube versions that have been manipulated to "sound better". I know a lot of Youtube songs that boost certain frequencies to sound "better" to the majority of the population with no regards to clipping or other issues.
The first step in identifying any issues would be exactly what CD you bought and from where exactly. Also, I can't overstate the importance of using AccurateRip in ripping any CD! It is a godsend! I personally spend a little bit of money to use dBpoweramp and take advantage of everything they have to offer.