Medicare bundle visit when administration code used

I have been having issues with medicare (New York downstate) paying us for our annual physicals or any E&M service visits when we give a vaccine and bill administration of a vaccine. I read that as of 01/13/2013 a 25 modifier must be added to the E&M code but when I do that it gets rejected from medicare saying a inappropriate modifier was used. Is anyone else having this problem and if so do you know how to fix. Thanks in advance