Bill,
Usually they want you to wait one year after the SCT before getting your immunizations. At that time, many clinics recommend re-immunization with the whole childhood barrage -- others don't. Until you reach that time, you will need to be careful. Make sure your family and those frequently around you get the vaccine, that will help a lot.
Are they more concerned with the vaccine because of the SCT or because of your ongoing treatment?
I had my auto SCT in August 2007 and had the first batch of immunizations in July 2008 -- still need to get my final batch. I don't remember for sure, but it seems like I did get the flu shot in the winter of 2007. Since the flu shot is not a live vaccine, there are less concerns with getting it than some of the others. You really shouldn't get any live vaccines.
Janet
PS - I live in a small college town and the students are back. There have already been reports of numerous H1N1 virus infections and they're concerned it will get worse. Sounds like I will be staying out of the main stream for a while.