Question #1 My tax softwared is allowing a loss on line 17, pg 1 of Form 1040 up to the $71k 2012 vested capital even though she has a $322 negative outside basis. Is this correct?
Presumably yes since the program should have used that additional contribution to allow the loss and then computed the basis with both the contribution and allowed loss in the basis total.
Question #2 Partner also paid $6k in unreimbursed expenses with arrangements with the partnership that she would not be paid back. The company did not take the $6k deduction on 2012 Form 1065.
Whether or not the partnership did or did not deduct anything this is still an additional capital contribution.
Caution may be needed not to record another (second) contribution for this amount when the partnership records the item.
Also, in order for a partner to claim unreimbursed expenses without reimbursement separately from the partnership accounting usually requires that is permitted by the partnership agreement. Many agreements may not allow or may require reimbursement of partnership expenses in the operating agreement.
For more detail see http://marcumllp.com/blog-tax-and-business/unreimbursed-business-expenses
"A partner cannot deduct expenses incurred on behalf of the partnership if the partnership would have reimbursed the partner for those expenses. The IRS has ruled that if, under the partnership agreement or practice, a partner must pay certain partnership expenses out of his or her own funds, he or she can deduct such expenses on the individual tax return."
Please ask if you need more discussion or clarification.