You might be experiencing an issue with the Tibial Nerve, the one that runs down the inside or medial side of the Ankle, where the Tarsal Tunnel is. The Tarsal Tunnel might for some reason, be intermittently causing slight impingement of the Nerve itself.
Presumably it is a muscle sensation, it's not just a slight throbbing that comes and goes within an hour, as I occasionally get those, they're called Vasospams, which are basically a fast repetitive twitching of a blood pathway, that are pretty harmless.
If it was anything vascular in origin, then avoiding any sort of caffeinated things, including Coffee, Tea, Guarana, Kola Nuts etc etc, might help, as one thing Caffeine does is Vasoconstrict bloodvessels, for a short time at least.
Perhaps it is when resting, you have some kind of specific foot position that's doing it, like reclining with the feet crossed, or one foot resting at a sloped angle, or propping one Leg on the other Knee.
When walking, I cannot say how the sesnation would occur, other than it must be either
A: Vascular in origin.
B: Nervous in origin.
It can't be due to any natural movement of connective tissue I would think, as I can't retionalise that in my mind.
Have you altered anything in your diet since, perhaps you made a change that coincided, and it might have been, you slightly reduced some sort of Vitamin or Mineral content in there.
For Vascular things, Minerals like Iron and Copper play their part, as does Vit C, an Iron booster. Also Calcium can in large amounts possibly affect Blood pathways, by I think causing some kind of hardening or stiffening action, I believe caused Calcification.
Maybe you might have to consider some kind of mobility exercises when you sit, like Ankle rotations, or mild Dorsi-flexion of the Ankles, I.E. movement up and down.