First off, this could be codec or bitrate related, Do you get the same problem with the same files playing from USB stick rather than the hard drive? if so, then there is unlikely to be a hardware problem with the drive.
Also thinking that if you ripped disks to the HD were they clean and scratch free? could the HD recording be damaged by interference during ripping process? do the blips occur in the same place in a track when replaying?
I've not noticed any problems with 128k MP3's copied from USB to the Hard drive, Or with Discs ripped to the Hard Drive (unknown bitrate).
Do you know what type of files were you playing, What bitrate they were and how did you transfer them to the drive?