Disphagia (the medical term for difficulty swallowing) is indeed something associated with MS. I would speak to your doctor about it.
Here is some information from the MS Society. (Clicking the link itself won't work. You'll have to cut and paste it into your browser's search bar).
http://www.nationalmssociety.org/Symptoms-Diagnosis/MS-Symptoms/Swallowing-Problems
I have problems swallowing and now have a g tube. I would let your doctor know and see a speech therapist they can diagnosis dysphagia and make recommendations for you.
I have swallowing problems, occasionally, usually with liquids and trying to get pills down.
My neuro usually puts me on a low dose of steroids for a week and increasing my baclofen until it goes away.