I think I know what the issue is. This has been discussed before and the short answer is that your raid or raid card, for some reason is having a problem keeping up with the media bandwidth required for proper playback.
The simple solution: If indeed this is your problem, and I think it is based on the symptoms you describe, is to replace the hard drives in your raid with drives that allow the bandwidth requirements.
If you have a raid composed of SATA drives:
It has been discovered that SATA drives that are over 50% full also tend to respond slower causing the symptoms you describe.
If you have a SCSI raid:
You may need to install more drives in your raid and only use 10K RPM drives. Slower SCSI drives (7,200 RPM) may work at times, but I don’t recommend them for this line of work.
If your drives are fine and provide the bandwidth needed for your media:
(this happened to me) you may have a slow raid card and will need to replace it so your bandwidth requirements are maintained.
Hope this helps,
Paul Thurston