I've never been on Rebif but was on Beta. Kinda similar side effects. I did also have the waves of crumminess and yes as I was increasing my dose they would get a little worse.
But, once I was on the full dose for awhile my body adjusted. I also had headaches. I have always had problems with those. I get them all the time.
Last weekend had one so bad that would not go away. Told my fiancee to either get me a pill or a bullet one or the other didn't matter. Luckily he came back with a pill.