I'm in Pediatrics and we come across this issue frequently.. per the American Academy of Pediatrics book "Coding for Pediatrics 2008" the administration of the vaccine includes:
Administrative staff services, such as making the appt, preparing the chart, billing for the service, filing the chart.
Clinical staff services, such as greeting the pt, taking routine vital signs, obtaining a vaccine history on past reactions and contraindications, presenting a Vaccine Information Statement (VIS) and answering routine vaccine questions, preparing and administering the vaccine with chart documentation and observing for any immediate reaction.
With that said, in order to code an E&M the service provided must exceed those services. When the nurse documents a significant and separate complaint or problem the additional reporting of 99211 is justified.
Even though my resource is a Pediatrics resource, I would think it would apply to all ages. In addition the modifier 25 should not be necessary because if the complaint/problem is significant and separate you should have another ICD-9 in addition to the V codes for the vaccine. We do get paid by commercial insurance without the modifier (side note: I audit these before they go out to be sure the nurse documented correctly to justify the 99211 because as always, if it's not documented, it was not done!)