Your S-Corp is not eligible for any refund since it did not pay a maxed salary and it is required to continue to withhold and match the social security tax until you reach the capped salary from the S-Corp. The cap applies to one person's salary, so the 2 separate businesses each treat the amount they pay you as a separate person's salary. From the business's perspective, you are one person to your primary job and a completely different person to your S-Corp. From your perspective, you are one person that hit the cap and will get your excess withholding refunded on your personal tax return.
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