You might be correct in that. I had a similar issue re my external HDD (a Seagate 1TB FreeAgent GoFlex). I've got lots of work files on it (Revit 3d model), which I'd open and work on. Then (an hour later) when I want to save the drive needs to be woken up (takes between 20sec an 1min depending on how W7 "feels" at the time). It actually was faster to unplug it and re-plug it into the USB port - would take no more than 5 sec to see the drive letter in Explorer, though that would sometimes stuff up file access rights - necessitating a reboot.
I tried every possible setting, including all the advanced stuff in power saving. None of them solved this issue. My solution (finally) was to write a DotNet app which simply re-writes a txt file on that drive every 10 sec. That way the drive never goes off. And BTW, this happened on my LapTop AS WELL as a Desktop, AS WELL as my work PC.
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