Perhaps you've answered your own question, eh?
Any cuff symptoms would be the result of whatever is going on. It could be that you lack scapular control on the affected side, due to thoracic spine immobility or weakness, thus making it difficult for the cuff to do its job.
Bilateral exercises may not be painful because the unaffected side can make up for the weakness a bit. That's not to say that you're still not causing further problems just because you're not feeling the pain.
Get back on your cuff exercises and see if it helps. Avoid painful exercises. If it persists, get it checked.
Bill