There a lot of variables here. The most obvious is that the jitter when playing 44.1 may be higher. Another is the digital filtering in the DAC, which usually sounds worse at 44.1. Another is the playback software, which has a large influence on the sound of playback of digital files. Another is the ripping software you used for the CD rips to hard disk.
FLAC files do sound a bit worse than native .wav, but you must really have a resolving system to hear this. Its not that obvious. I doubt if this is the problem.
I would recommend to first do the easy stuff, namely the player and ripper. See this for recommendations:
http://www.empiricalaudio.com/computer-audio/
Steve N.
Empirical Audio
FLAC files do sound a bit worse than native .wav, but you must really have a resolving system to hear this. Its not that obvious. I doubt if this is the problem.
I would recommend to first do the easy stuff, namely the player and ripper. See this for recommendations:
http://www.empiricalaudio.com/computer-audio/
Steve N.
Empirical Audio