I have two theories apart from the nerve one

Relative stiffness, some muscles are more powerful than others and hence the brain recruits them more and shuts down their antagonist or synergist. Which in turn recruits other antagonists which cause more issues.
For instance, pec minor in forward hunched over posture which acts against lower traps and overpowers serratus.
To counter that, lats are recruited, which hunches you even more and pec minor gets reestablished.
This theory holds that over time, either with stretching or constant vigilance, you can mitigate the effects.

Since exercising for TOS is often shoulders back and down (for lower traps), it ends up recruiting lats too which is a problem.

Second theory, is of some sort of internal trauma which is being masked by these muscles. I think that may be wrong, because sometimes the right muscles kick in and the pain goes down.