Hello, I am late to this discussion but I've been experiencing a quick rattling or clicking sound on my Windows 7 VM within Parallels 11 (latest update) on El Capitan (latest update) on a mid-2009 13" MacBook Pro.
I recently upgraded my 500GB HDD to a 524GB SSD (Crucial) without issues. Whenever I tried accessing an item (opening a folder or a file) within Windows Explorer, I would hear a hissing rattling thing. Since SSDs have no moving parts, and the components work at low voltages anyway, power hum is out of the question.
Today I was copying a PDF file from my Windows 7 VM to a USB drive. The rattling appeared for half a second. I tried a different tack: could it be Parallels audio controller? After reading the comments on this thread, I tried a second thing: right clicked on Sounds and opened Sound Schemes. Then I clicked PLAY on each enabled sound for each action within that scheme. I couldn't find the rattle, but I disabled some fax-related sounds and other things I don't use, clicked Apply and closed the dialog box.
The rattling/clicking sound is gone! Once again, a low-tech solution to a big headache. Hope it helps someone.
Mario