For me, both vaccinations as well as viral infections, can amp up my immune system and cause an autoimmune flare.
Some of the companies making the killed virus H1N1 vaccine shot have added ajuvants that also amp up the immune system in a nonspecific manner. Some formulations do not contain ajuvant.
The live virus flumist vacc is unajuvanted, but it is only for healthy folks. Certainly anyone who is on an immune-system modifying medication should be wary of live virus vacc.
I'm taking my chance & not planning to get vacc'd, however if I did, I would want an unajuvanted shot, preferably one without thimerosol, since mercury is linked to autoimmunity. I'm not sure that option is available.
Probably the most sensible thing is to do one's research & discuss the options w/your HCP.
Best wishes.