Not sure if this is the same, but I had extreme soreness on my right shoulder when I started squatting 2-3 weeks ago. I started at 135, then reset to 115 to fix form issues and because I kind of tweaked my back on my first 10 lb jump attempt. My right shoulder didn't hurt much until it touched something -- then it hurt quite a bit.
I seem to have fairly extreme flexibility issues. If I don't warm up and stretch, especially when working out at the beginning of the day, I can't assume the squat position at all. Like my grip would have to be so wide, it's on the plates. I don't really have time to warm up, so I started doing my first empty set doing exactly that. By my second empty set my hands can get to just barely inside the hooks, and I have to be careful to not crush my fingers racking the empty bar. By my first weighted set my hands are still too wide but far better. Etc -- I keep bringing my hands in every warm-up set. By my working set they're pretty good.
I still noticeable tightness in my shoulders during the day I squatted, but I don't have any pain any more -- and I'm up to 180 in a couple of weeks