How does ReplayGain affects Flac files? Options

[hermes_vb]

Let me explain what I mean. First of all I'm new to Flac. I did some reading and decided to backup my entire CD Collection to a lossless format to avoid loosing more CD's due to scratches, laser burns, etc. After several rips, I decided to play some of the albums, and it seemed to me that the obtained audio, although crystal clear, was kind of low when compared to the original source. To eliminate possible playback variables, I burned a CD from Flac files (using Nero) and compared the new CD to the original one by playing them both in my Bose system (with the same audio settings). Again, it seemed to me that some songs sounded a little lower than the original CD although not all like the Flac vs CD test. Is it just me or ReplayGain causes some kind of permanent alteration?

PS I Ripped with CDex v1.51, playback with Foobar v0.8.3 and encoded with Flac Frontend v1.12 using parameter string:

-8 -V -T artist="%a" -T album="%b" -T title="%t" -T date="%y" -T tracknumber="%tn" -T genre="%g" --replay-gain -o "%2" "%1"