I thought I would throw this one out there since it's recently affected my running on a small level. A couple weeks ago I noticed I was developing a small bump at the base of my anterior tibialis tendon after a long run. Getting old is such a great thing isn't it?! It hasn't really been painful but the bump will snap up and down if I have my shoes laced tightly. It's a synovial sheath irritation in the slick layer that allows the tendon to glide smoothly.
Ultimately, excess lacing tightness is what caused the bump to form. I have a habit of really cinching down on my shoe laces and this caused some increased stress on this area. Now, if I was to over-tighten the laces, it would cause the little bump to snap up and down under the laces and eventually swell even larger. So that's clearly not ideal. The repetitive snapping is annoying and might become painful with enough exposure. I'm not waiting to find out. Another factor that could contribute is frequent uphill running because it would cause you to increase the use of the anterior tibialis muscle and tendon, close the ankle joint up further and increase the friction across the front of the tendon against the shoe. My right foot collapses inward slightly more so the tendon may experience slightly more stress from that as well.
As a result I've done a slight modification to my lacing pattern to relieve the area of its pressure. By changing the lacing pattern the bumped area reduced significantly in swelling and overall size. Applying ice is another good measure to help decrease localized swelling and pain.
These types of bumps will also sometimes occur at the Achilles tendon from the heel cup of the shoe rubbing the tendon repetitively. In any case you could modify the shoe by cutting out a small portion of the heel material that is rubbing or get into another pair of shoes that doesn't stress the area.
Please let me know if you have any questions about shoe lacing patterns or tendons forming mysterious bumps at email@example.com.