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I entered $2500 stipend in 1099-MISC field in wages. I ran smart check & it shows I need to check the link to schedule C. I check box & my refund goes down $1053. Help??

This is strange because everything works smooth until I get to smart check.  Once I am asked to choose which schedule for box 3 on the 1099-MISC form, the refund goes down over $1000.  That would seem that I am paying 42% tax on that stipend.  It seems that I must be doing something wrong.  Are there different forms that I have messed up on?  I have read the steps on how to properly input a 1099-MISC.  When I delete the 1099-MISC the refund goes back up.  When I re-enter the 1099-MISC the refund does not change until I get to the Smart Check portion of Turbo Tax.  I am happy to pay the taxes if that is what I owe, I just want to check and see if I have done something wrong.