My girlfriend's PC is an amalgamation of old and new parts. The ten-year-old motherboard went south and needed replaced, but the IDE hard drives were still in good shape. Seeking to merge the old with the new, it was upgraded from a 750MHz AMD Duron processor on a decade-old Gigabyte motherboard (hot when AGP first debuted) to one of the newer Intel Core 2 Duos with a Gigabyte S-Series motherboard. IDE is on the way out, replaced by Serial ATA, so I had to look specifically for that in whatever motherboard I was going to buy.
We put the thing together, fired it up, installed Windows XP Pro, got everything else on there, and she started happily plugging away on the upgraded monster (slipped a Geforce 7950GT in there to replace the 3dfx Voodoo3 too, to feed her growing gaming habit). Everything seemed ready to cook.
As an avid online-TV watcher, it wasn't long before she discovered the sound and video in the stuff she was watching would stutter often, though it seemed to smooth out as things played on. I initially chocked it up to buffering issues, but when it started happening in offline videos and music in Windows Media Player and iTunes, I knew something was amiss.
We tried updating sound hardware drivers, but that didn't help. Then we defragmented the hard drive, but to no avail. I even replaced the IDE cable, but nothing changed. I had narrowed it down to only happening when the C drive was being accessed, though. She tested it by playing a video file, then in the middle of it, she initiated a file copy from her laptop through the LAN to the afflicted machine's C drive and sure enough, as soon as the HDD activity LED lit up, the sound started getting choppy. Even Windows start up and shut down sound events were affected.
After a few minutes of tireless searching (hey, I'm good), we stumbled onto a couple very specific fixes other users fighting this problem had reported.
The first was to see if Windows had reverted the Transfer Mode between the hard drive and motherboard from the more common and faster DMA back to the slower but more reliable PIO. Windows switches automatically to PIO after a number of disk errors are reported, as it's apparently a more stable reading method. Problem is, since it is slower, it can cause glitches like what we were experiencing, and it's particular to IDE drives, so I wouldn't have seen this before on our other machines, which use SATA exclusively.
To check for this, go to Settings-> Control Panel-> System-> Device Manager-> IDE ATA/ATAPI Controllers-> Primary IDE Channel-> Advanced Settings. Look under Device 0 and it should be set to "DMA if available." If it says "PIO only" instead, change it, click OK, save settings, and reboot. This may resolve your issue, though if the disk is really going bad, Windows is likely to change it back to PIO after some time, and you may want to look into getting a new hard drive.