Simontju 02-03-11: I did my "fun" experiment using relatively powerful CPU - Intel Core i7 950 3.06GHz (Quad Core), ASUS Rampage III motherboard with SATA3, 12 GBytes of RAM and a SATA3 Hard Drive etc - hardly a typical "slow" computer having audible problem in FLAC processing.....Simon, if by any chance you have your SATA3 hard drive connected to the Marvell 6gbps SATA3 controller on your motherboard, be aware that that controller tends to be highly erratic, based on my experience and many other experiences which have been reported on the net.
I obviously can't say that that was the reason for your findings, but I certainly would not rule out the possibility. I suggest that you look at the Windows Event Viewer, and see if there are a large number of errors indicated that might be hard drive related.
A few months ago I built a computer which also uses an Asus X58 board (the Sabertooth), and the same i7-950 cpu you are using. I initially connected the SATA3 SSD I am using as the "c" drive to a Marvell 6gbps SATA3 port. After spending several days trying unsuccessfully to troubleshoot enormous numbers of errors indicated in Event Viewer, and frequent bsod's and crashes, I switched the SSD to an Intel 3gbps port, and the computer has been rock solid ever since.
If your audio file was located on your "c" drive, and if that drive was connected to a 6gbps port, keep in mind that while you were listening this issue could have affected not only the reading of the audio data from the drive, but the operation of Windows and your audio program as well.
Regards,
-- Al