Strengthening Healthcare Options for Vulnerable Populations Act - Amends part C (Medicare+Choice) of title XVIII (Medicare) of the Social Security Act (SSA) to extend permanently the authorization for certain Medicare Advantage (MA) Dual Special Needs Plans (D-SNPs).

Requires MA D-SNPs by December 31, 2018, to be fully integrated, in accordance with state law, with capitated contracts with states for any benefits under SSA title XIX (Medicaid), including long-term care and behavioral health.

Directs the Secretary of Health and Human Services (HHS) to develop a clearly defined role for state Medicaid agencies in contracting and oversight of plans.

Directs the Secretary, in implementing requirements for the payment of Medicare+Choice organizations, to take steps necessary to ensure that the quality rating for a D-SNP: (1) does not disadvantage a plan that enrolls full-benefit dual (Medicare- and Medicaid-) eligible individuals, qualified Medicare beneficiaries, and individuals with complex health care needs; and (2) accounts for differences in socioeconomic and demographic characteristics of enrollees of such a plan that result in significant variation in health outcomes.

Allows the Secretary to increase temporarily the quality rating that a specialized MA plan would otherwise receive under certain circumstances.

Directs the Comptroller General (GAO) to report on steps taken for improving health outcomes, cost controls, and beneficiary satisfaction.

Amends the Patient Protection and Affordable Care Act to designate the Federal Coordinated Health Care Office (FCHCO) as the dedicated point of contact within the Centers for Medicare & Medicaid Services to assist states with ongoing D-SNP administration issues.

Allows the Secretary, through the FCHCO, to waive applicable Medicare requirements to promote the integration, alignment, and delivery of items and services under the Medicare program and the Medicaid program, with respect to dual eligible individuals and to ensure the seamless delivery of patient-centered services across the continuum of care with resect to such individuals.

Requires D-SNPs to provide coverage during the appeals process with respect to dispute resolution for claims.

Directs the Secretary to establish a streamlined process for dispute resolution for claims and appeals, with respect to items and services furnished to special needs individuals, to align the Medicare program process with the one under the Medicaid program.

Amends SSA title XI to require the Secretary to report to Congress on the Integrated Data Repository and the One Program Integrity System.