3 years ago I partially tore my spring ligament, tibialis posterior tendon, and I can't remember the name of the ligament but another ligament in my ankle was beginning to show signs of a tear. These injuries were from running as part of my college cross country team. I wore a cast for 3 weeks and then wore a boot for I believe it was 2 months. However, the pain has never completely gone away. Over the years it has stayed persistent and worsens the more I'm on my foot. Its not just activity that irritates it though, I have a desk job and a lot of times at work after a couple hours of sitting it will start to hurt. The pain is normally a dull ache which is pretty constant but sometimes the pain is very sharp. Also the arch on that foot feels different when I'm pressing on it than the other foot. What could be wrong?
Unfortunately, several things could be wrong. You could still have posterior tib tendon inflammation. If you do, you may have some chronic tenosynovitis or even microtears within the tendon itself.
The spring ligament and the other small ligaments in the longitudinal arch do heal, but they heal with scar tissue. Scar does not flex and stretch as well as the original ligament. So, that changes the biomechanics in the foot.
You probably also injured to deltoid ligament on the medial side of the ankle. The posterior tib tendon swing just inferior to the deltoid as it passes the ankle. This ligament could have done one of two things. In some patients, it heals with scar and is very stout. While in others in heals in a lengthened position, which can lead to chronic instability. The chronic instability allows the ankle to wobble, while the tight ligament can sometimes make the ankle too tight.
Because of the tight ligaments, you could be developing degeneration of the articular cartilage between the small bones of the midfoot and ankle.
All of this could be setting up some inflammation. Which is why you probably develop the deep achey feeling after a period of rest (sitting). The inflammation causes the joints to "gel", or stiffen, thus the cartilage doesn't get the fluid it should. The joint fluid nourishes the cartilage, so if it is not bathing it, the cartilage sort of cries out, and starts to hurt. (Some people have this problem in their knees and they have problems sitting with the knees bent for long periods, like in a theater or long lecture. Same effect.)
What's bad about this is that some times, there is not too much you can do about it. You can try the NSAIDs (if you have no medical problems which preclude their use), but they have to be taken regularly, around the clock, not on an as needed basis. You should always have good longitudinal arch supports. Avoid flats or flip-flops. They don't have to be custom made, just comfortable. Some patients swear by the joint supplement medicines (glucosamine, chondroitin sulfate, and hyaluronic acid). You could give them a try. Maintain your range of motion in the ankle and foot. Try to do nonweight bearing physical activity, such as swimming or biking whenever possible.
If the pain is such that you just can't take it anymore, then you should probably seek an orthopedic foot and ankle specialist. There is a new technique for chronic tendon and ligament problems, called Platelet Rich Plasma injections. It is still in the experimental stages, but some of the early research is promising. Besides this, the foot and ankle specialist may have some tricks up his/her sleeve.