My personal take on this...
I have a stretched cruciate ligament (or it tore off and dissolved, simply don't know) in my knee that gives me problems sometimes. Ligament laxity from an injury can give you occasional pain or discomfort, but there is a 'real' and a TMS component.
When ligaments cannot give (enough) support to a joint, muscles and other structures have to make up for it to not dislocate or damage things. It is my believe that this is what can give you real pain, because the muscles and other structures aren't always capable of doing that for several possible reasons; they are meant for other loads, they are suddenly loaded when the muscles are off-guard, or they are simply not capable of holding the load. They start to inform the brain with sensory information with the purpose of you taking it easy so you can prevent further injury. The TMS component is that your mind/body overreacts to the signals these muscles and other structures give; the pain is more intense, muscles start to cramp up more and sooner as fear sets in (sometimes even before you even started!) and the aftermath/reaction is more intense and takes longer to resolve. So for me it is accepting the real component and minimizing the TMS component. Using my knee intensively will give a reaction, it starts to click, grind and surrounding muscles may cramp up, but it should resolve in a matter of days. Fear of using my knee (during or afterwards) always makes things worse than they should be. Being able to differ between the two components is a matter of experience and time.
So, to conclude: Yes, old injuries can have lasting effects that serve a good purpose of protecting certain structures, but TMS can make these effects much more intense than they should be.