Figured out my own question after Sampsonmines gave me the key. TurboTax for Home and Business asks you about your business financial data before your personal. Within business, it asks for your income before your expenses.
In this scenario, I only had $10K of income (a grant) and started with zero expenses, so my "apparent" refund was based on an Earned Income Credit at that low income level. Every time I entered an expense, my expense deducted from my income, lowering my AGI, lowering my refund!
The whole picture isn't told until you do your LLC and then your personal taxes.
Tim
