I ran into what seems to be a tk2d bug, but I found a way to fix it in my case. I was using custom box colliders on some of my sprites in one of my tk2d sprite collections. The colliders were working fine when the game was running, but later I adjusted some colliders in that same sprite collection on some different sprites, and then all of a sudden the box colliders on my aforementioned sprites suddenly would not work anymore during runtime.
After trying all kinds of things, I found a way to fix the problem: Select the game object in the Hierarchy, and then in the Inspector change its sprite to a different sprite and then switch it back to the original sprite. After I did this for each of my faulty sprites, then they worked perfectly once again. So if someone has a tk2d sprite with a custom box collider that suddenly will not work correctly during runtime, then try switching the sprites in the Inspector and see if that fixes the problem. I hope this helps anyone who runs into this problem.