I had to deal with the same problem a while back (somewhere halfway dec last year). I constantly had problems with the second HDD not beeing recognised (and later on both disks not recognised at times). When i installed a little program to monitor the HDD's temperature i noticed these were constantly around 48% celcius and gettin over 50/52 if used intensively for a little while.
First thing i tried was one of em frontbay fans, the white one shown in Adeptus's post (it has two little fans). It didn't get it down enough. Then i went and put a HD cooler on (under) both harddisks..the cheap blue thingies shown in Kao's post (could be another brand, but that's what they look like). That did the trick and the temp of my HDDs now stays between 28-35 degrees celcius.
So, if anything...get them blue HD cooler(s) on
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