Medicare IVIG Access and Strengthening Medicare and Repaying Taxpayers Act of 2012 - Title I: Medicare IVIG Access - (Sec. 101) Directs the Secretary of Health and Human Services (HHS) to establish a three-year demonstration project under part B (Supplementary Medical Insurance) of title XVIII (Medicare) of the Social Security Act (SSA) to evaluate the benefits of providing payment for items and services needed for the in-home administration of intravenous immune globin (IVIG) for the treatment of primary immune deficiency diseases. Requires the Secretary to enroll up to 4,000 Medicare beneficiaries who have been diagnosed with primary immunodeficiency disease for participation in the project. Requires that generally items and services for which payment may be made under the demonstration program be treated and covered under SSA title XVIII part B in the same manner as similar items and services covered under that part. Directs the Secretary to establish a per visit payment amount for items and services needed for the in-home IVIG administration based on the national per visit low-utilization payment amount under the prospective payment system for home health services under Medicare. Authorizes the Secretary to waive such Medicare requirements as may be necessary to carry out the demonstration project. Specifies requirements for interim and final evaluations for Congress of the impact of the demonstration project on Medicare beneficiary access to items and services needed for in-home IVIG administration. Requires the final report to Congress to: (1) analyze the appropriateness of implementing a new payment methodology for IVIGs in all care settings under Medicare part B; and (3) update the report entitled "Analysis of Supply, Distribution, Demand, and Access Issues Associated with Immune Globulin Intravenous (IGIV)," issued in February 2007 by the Office of the Assistant Secretary of HHS for Planning and Evaluation. Makes specified funds available for the project from the Federal Supplementary Medical Insurance Trust Fund. Title II: Strengthening Medicare Secondary Payer Rules - (Sec. 201) Adds requirements for determination through a Centers for Medicare and Medicaid Services (CMS) website of a final amount for reimbursement to the appropriate Trust Fund for a conditional Medicare secondary payment in the event that a beneficiary's primary plan proves to be responsible. Allows a Medicare claimant or applicable plan, within 120 days before the reasonably expected date of a settlement, judgment, award, or other payment, to notify the Secretary that a payment is reasonably expected and the payment's expected date. Directs the Secretary to maintain and make available to Medicare beneficiaries (and to authorized family or other recognized representatives and to an applicable plan which has obtained the beneficiary's consent) access through a CMS website to information on claims for items and services, including those relating to a potential settlement, judgment, award, or other payment. Prescribes requirements for such a website. Deems to be the final conditional amount subject to recovery related to a settlement, judgment, award, or other payment any statement of reimbursement amount an individual downloads from the CMS website during a specified protected period, if the settlement, judgment, award, or other payment is made during the same period. Prescribes requirements for resolution of discrepancies with a statement of reimbursement amount. Directs the Secretary to promulgate regulations establishing a right of appeal and an appeals process with respect to any payment determination for which recovery of conditional payments is sought from an applicable primary plan. (Sec. 202) Creates an exception to the requirement that a primary plan (and any entity receiving payment from a primary plan) reimburse the appropriate Trust Fund for any Medicare payment with respect to an item or service if the primary plan has or had a responsibility to make the payment. Declares that this repayment requirement shall not apply with respect to any settlement, judgment, or other payment by an applicable plan arising from liability insurance (including self-insurance) and from alleged physical trauma-based incidents (excluding alleged ingestion, implantation, or exposure cases) constituting a total payment obligation to a claimant of not more than a single threshold amount calculated by the Secretary for the year involved. Directs the Secretary to calculate and publish a single threshold amount annually according to a specified formula (excluding ongoing expenses). Requires the Secretary to report annually to Congress on the single threshold amount for settlements, judgments, awards, or other payments for conditional payment obligations arising from liability insurance and alleged incidents, but also on the establishment and application of similar thresholds for conditional payment obligations arising from worker compensation cases and no fault insurance cases. (Sec. 203) Changes from mandatory to discretionary the civil monetary penalty of up to $1,000 for an applicable plan that fails to comply with requirements for determining if a claimant is entitled to Medicare benefits and for submitting to the Secretary for each day of noncompliance with respect to each claimant related information by or on behalf of liability insurance (including self-insurance), no fault insurance, and workers' compensation laws and plans. Directs the Secretary to publish a notice in the Federal Register soliciting proposals for the specification of practices for which sanctions will and will not be imposed (safe harbors). Requires the Secretary, after considering the proposals submitted, to publish in the Federal Register, for comment, proposed specified practices for which such sanctions will and will not be imposed. Requires the Secretary, after considering any public comment, to issue final rules specifying such practices. (Sec. 204) Requires the Secretary to modify insurance information reporting requirements so that an applicable plan, in complying with them, is permitted but not required to access or report to the Secretary beneficiary Social Security account numbers or health identification claim numbers. Requires extension of the deadline for such modification by one or more periods of up to one year each if the Secretary notifies appropriate congressional committees that the prior deadline, without an extension, threatens patient privacy or the integrity of the secondary payer program. (Sec. 205) Sets a three-year statute of limitations on a Medicare secondary payer claim by the Secretary for reimbursement against an applicable plan that becomes a Medicare primary payer pursuant to a settlement, judgment, award, or other payment made relating to the payment owed.