I'd have to agree with corebreach in that there should be no difference between the CD and the FLAC copy. I also use FLAC for all my audio files. I've listened to the original CD vs. the FLAC streaming from my PC, and can tell no difference. Perhaps you are using an analog out from your PC, or perhaps there is some type of processing going on in the PC that's not occurring in the original...
As to sound cards, it sounds like you are going using an analog output from your PC (again, that might explain a difference between FLAC and CD -- you're using two different DACs for playback comparison). Many of us use digital out from PC to preamp, and allow the DAC stage to occur there. There are many fine preamps on the market that will do a better job of digital to analog conversion than most PC sound cards. That said, there are nice sound cards out there, but I've never been too interested in researching them -- not only because I believe that my preamp has a better DAC than almost any sound card, but also because surround decoding can be handled so much better by a dedicated preamp (i.e., watching movies). Actually, I've never played much with movie decoding software for sound cards, but if the sound card software that I've used (from a variety of manufacturers) is any indication, there will remain much to be desired. Anyway, going digital out to a preamp is the only way to go, IMHO.
As noted above, redbook CD is only a 16-bit data word. You can upsample it, and you can upscale it, but it's still only 16 bits to start. It may be possible to get a little more resolution out of it by these methods. Again, these can be achieved in many home theater receivers and processors. My old Outlaw would do a 24/96 mode, I believe. It sounded pretty good, for the most part. My Cary doesn't upsample, but it sounds great nonetheless.
There are many options out there. Good luck!