Multiple Sclerosis (MS): This is a common cause of elevated CSF protein, particularly in young females. MS can present with a wide range of neurological symptoms, including headaches, and is known for its unpredictable course. The presence of intractable headaches could be indicative of an MS relapse or a pseudo-exacerbation.

Chronic Meningitis: This condition can cause elevated CSF protein levels due to the chronic inflammation of the meninges. Symptoms can include headache, fever, and stiff neck, among others. The chronic nature of the condition could explain the intractable headache.
Guillain-Barré Syndrome: Although more commonly associated with ascending paralysis, Guillain-Barré Syndrome can also present with elevated CSF protein. Headache can be a part of the initial presentation, especially if there's significant spinal cord involvement.
Spinal Cord Tumors or Cysts: These can cause elevated CSF protein by obstructing CSF flow or directly producing protein. Symptoms can include pain, weakness, and sensory changes, but headaches can occur, especially if there's associated hydrocephalus or increased intracranial pressure.

Subarachnoid Hemorrhage: Although typically presenting with a sudden, severe headache, some cases can have a more gradual onset. Elevated CSF protein can be seen due to blood in the CSF. Missing this diagnosis could be fatal.
Meningeal Carcinomatosis: Cancer spread to the meninges can cause elevated CSF protein. This condition is critical to identify early due to its poor prognosis and the need for specific treatment.
Infectious Meningitis (Bacterial, Viral, Fungal): These infections can cause elevated CSF protein and are medical emergencies. The presentation can sometimes be atypical, especially in immunocompromised patients or with less common pathogens.

Neurosarcoidosis: A rare condition where sarcoidosis affects the nervous system, potentially causing elevated CSF protein. Symptoms can be varied and include headaches, among other neurological manifestations.
CNS Lymphoma: Primary central nervous system lymphoma can cause elevated CSF protein. It's more common in immunocompromised individuals but can occur in anyone, presenting with a range of neurological symptoms including headaches.
Tuberculous Meningitis: Although rare in some populations, this condition can cause significantly elevated CSF protein and is critical to diagnose due to its treatability and potential for severe neurological sequelae if missed.