I had all my kids (ages 4, 8, 10 & 12) vaccinated last Monday (what fun that was!!). They had both the H1N1 and the regular infuenza vaccine. None of them had any side affects from the vaccines.
My whole family (me, husband , non-DMD son and DMD son) was vaccinated over a week ago, when the vaccines first came out. None of us had any problems. Make sure you get the injected vaccine, not the nasal flumist given your chronic condition (and immunosuppression?) I wouldnt be too concerned about side effects