You are correct that an S Corp shareholder would not be considered Self-Employed and file a Schedule C.
Are the income/expense items in the same lines as in prior years on your Form K-1?
Are you sure 'self-employment' is the reason for the upgrade, since Premier can also handle self-employment. Can you choose not to upgrade, and Continue?
Since we can't see your return in this forum, I would suggest you Delete your Form K-1, clear your Cache and Cookies and re-enter your K-1.
Click this link for more info on Entering Form K-1.
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