I think it can take 6 months for the meds to really take affect like Sally said.
When i started Avonex, I had a terrible time after the shots, it actually made a lot of my symptoms feel worse, especially my vision and the pain. I think the vision was from the fever I would get about 4 hours after the injection, and the pain was the flu like symptoms. Would be in some weird spots like side of my ribs, spots i never had pain before.

Such problems have subsided since i stopped having side effects, but like others have said sounds like it can be the MS hug. Take it up with your Neuro when you see them.

The injection sites can be having a reaction where they are red since Rebif is administered just under the skin.

Hope everything gets better for you!