The endoscopy see the anatomical details, while the barium esophagogram show the movements of the food pipe which can't be seen by the endoscopy. The causes of swallowing difficulty can be;
1) Mucosal injury (internal lining of pharynx and esophagus) may be caused by potassium chloride tablets, nonsteroidal anti-inflammatory drugs (NSAIDs), or antibiotics (doxycycline, tetracycline, clindamycin, trimethoprim-sulfamethoxazole).
2) Pharyngeal diverticulum
3) Peptic strictures due to reflux
4) Benign esophageal tumors
6) Esophageal Stricture or constriction
7) Globus; a psychological phenomenon of something causing difficulty in swallowing (there is a condition called as Globus sensation, which may be responsible for the symptom of problem in swallowing). Please read this resource;
Globus is quite a common phenomenon and many times can be associated with anxiety.
Following investigations are necessary for the work up;
1) Fiberoptic endoscopic evaluation of swallowing and upper gastrointestinal endoscopy. This has been done for her.
2) Esophageal manometry (pressure study of the food pipe).
3) CT scan
4) Barium swallow
This will give you the exact cause of your symptoms.
Autoimmune disorder present with wide symptoms like joint pain, muscle pain, fatigue, etc. Please read this article about the esophageal motility disorder. This is technical but is likely to give you an overview of the problem;
Please feel free for your follow up questions.
I would be happy to assist you further, if you need any more information.
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