Some things to consider:
In my experience, which may or may not apply to you, many people tend to have their shoulders somewhat internally rotated. If when you stand without thinking your thumbs point inward instead of forward (i.e. parallel to each other) then to some degree probably there is internal rotation of the shoulder joint. This then means that the joint tends to become annoyed by use. Rest will allow the inflammation to settle down, but if the alignment issue has not been dealt with, then returning to working out will tend to annoy it all over again.
Why does the shoulder joint get internally rotated?
Typically because the hips are tilted forwards.
Why do the hips tilt forwards?
Typically because the hip flexors are tight and the muscles complementary to them (glute and one of the heads of the hamstring) have lost the ability to execute peak contraction movements well.
There is more to this analytical framework, but perhaps those thoughts may serve to help you find the cause and solution of your particular issues.
On our PTP a couple years back you pointed out how much my natural gait and stance and alignment on my feet point outwards, the exercises you gave me seemed to have helped a lot. I screwed up my left hip badly in a parachuting accident back in my twenties and tore my left ACL in a Judo accident in my forties, so I seem to be highly asymmetrical from the waist down, it probably throws off my whole structure. I should do more alignment work.
If you can swing it, I highly recommend the PTPs to anyone out there, by the way. Guro Crafty tailors the teaching to your interests and skill level.