If you're billing the components correctly, you should be getting a higher reimbursement than the old system. It would be inappropriate and considered illegal to knowingly bill the wrong code to receive higher reimbursement. Just to go over the differences in the code sets, though...
90471-90474 are based on the # of physical administrations that you give, not how many vaccines you're giving. So, for example, if you were giving an MMR, and DTaP, and an influenza vaccine, you'd bill three administrations: 90471, 90472, 90472.
Now, with the pediatric vaccine codes 90460 & 90461, you bill for the administration of each component of the combination vaccines, regardless of how many shots are given. Each vaccine product with a CPT code is reported with 90460, and vaccines with multiple components (combination vaccines) also get 1x 90461 for each additional vaccine product contained in the combination. So, sticking with the example from above, the admin codes would be billed like this:
[MMR CPT]
90460 (Measles)
90461 (Mumps)
90461 (Rubella)
[DTaP]
90460 (Diptheria)
90461 (Tetanus)
90461 (Pertussis)
[Influenza]
90460 (Influenza)
(I don't have my book with me, and I don't have those vaccine codes memorized). Insurers require the codes to be sequenced in this manner, to easily distinguish which admins go with which vaccines. Many are still inappropriately denying correctly billed codes as duplicates, but they should reprocess the denials, when asked. You are paid less for the 90461's because the only represent a portion of a single administration, and you've already been paid for the bulk of the work in 90460. Hope that helps!