The hard disk had been upgraded at some stage in the past an was not touching its heatsink.

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Yeah, the hard drive's heat spreader only contacts 12.5 and 17mm drives; the 9.5 that was likely installed wouldn't reach it. It's not a huge deal, unless you're running a Hitachi or Toshiba hard drive. I use Fujitsu or Seagate Marathons (or >9.5mm drives) in mine, and have had no problems.