That's why I was so confused earlier, these 2 songs aren't from the same CD.
It's not the mp3 rip itself that caused those differences, or the ripper him/herself, but the original on the CD is different than the other original the FLAC is sourced from. Which is why I said those compilation CD's are often different, as they wanna mix it up a little because they know some people might already know the original.
I usually listen with replaygain on, and once those 2 tracks were matched, the vocals were more or less the same volume level, but there's quite a dramatic difference in the synths (in terms of volume and programming).
It certainly sounds like they went to eleven with the synth's on the mp3 version, some of it is reprogrammed and there are indeed extra layers (LAYERS, THANK YOU OHHGOURAMI, THAT'S THE WORD I WAS LOOKING FOR LOL).
And about the synth sounding like distortion, it's worthy to note that electrostatics and ortho's are pretty much unbeatable in terms of speed. The HD800 is real quick too, but I guess it's treble happiness messes things up with this type of song, it ain't worth the pain =P. That's pretty much why me and ohhgourami heard it properly as a layer of synth, and not just some grainy distortion.
I'm sure the soundcard is fantastic for what it is, but it's incomparable to a proper DAC. The soundcard used the AK4358 with a THD spec of -94db or so, whereas a top of the line Sabre32 chip has a vanishingly low THD of -120db, that's many orders of magnitude lower, and keep in mind the differences in power supplies and analog sections.