HP 530 laptop running Ubuntu Mate 18.04 makes a clicking/tapping noise every 3 seconds. Replaced the hard drive, the newer one made a similar once-off tap on startup then was quiet. This pattern went on for a while, then the same regular clicking noise started again. I tried booting to a USB stick, then it was quiet - so noise appeared to be coming from the HDD. How likely is it that two consecutive HDD's will develop the identical problem, unless the cause lies elsewhere?
When dual-booting into Windows it’s quiet. As soon as the machine boots in Ubuntu, before any apps start up, it clicks. When the speakers are muted it still clicks, but when a video is played with sound set low, the clicking disappears. As soon as the video is paused, clicking recommences.
It's also quiet when music is played and quiet when playing videos in YouTube. Clicking consistently resumes when play is paused.
Having said all of that, the conclusion appears to be that the problem is a software issue being caused by Ubuntu 18.04 Mate.
I have similar problem with regular double burst of noise from left speaker. Have resorted to plugging in to headphone jack to divert noise. Has bug report been raised?
Have problem with 18.04.3. Didn’t happen with 18.04.2 except for one burst during startup.
Change Hard drive, Your hard drive has probably aggressive power management or other kind of firmware related staff ... this is why I avoided in the past some Western Digital laptop HDD, all have that annoying clicking, on newer generation WD fixed this.
This is also characteristic to OS, if system is boot on that hdd or is connected over USB, over USB might get aggressive power management.
Of course under Linux you can customize manually the hdd behavior...
And of course, my explanation apply if I understand correctly your issue ... not related to system background work, hdd head random move to prevent "wear" on plattern,..
I just give you the tip ... more you can search on internet ... or return to using Windows