Just when I thought I'd hit a sweet spot!

I've recently swapped my main storage drive from an F3 to a WDEARS. The F3 is still connected, but is asleep most of the time (backup drive).

I've had a couple of good days with the WD as my temp/storage drive, but have just put my headphones on (plugged into my R3's headphone socket), and between songs, I can hear a distinct static 'seek' noise through my headphones every time the HDD light goes on.

The F3 is fast asleep, and the WD is awake and has my music and temp directory on it.
The only thing I've changed is swapping the F3 with the WD.

What gives? Any ideas?

The noise you get may well depend on how much the signal is attenuated. Try therefore to set all the program-specific volume controls near the maximum and to dial down the one specific to the soundcard which controls the overall volume it outputs. With luck, that will have an effect on noise. If you have an analog volume control, set all software volume controls near the maximum and use the analog control: that will definitely work.

Try not plugging your headphones into the R3's socket. If that works and you want to keep using it, you'll have to check the cable that leads to it and protect it from interference.
If it doesn't work, you could also use a cheap USB soundcard to get rid of the noise. Take care to choose one designed to work with headphones.

Different headphones have different technical characteristics and might be a better for your computer.