I've always requested a waiver of the total amount, and ProSeries has always filled out the form as the instructions require.  Your results may vary with ProConnect, although I doubt it. 

Waiver of tax for reasonable cause. The IRS can waive part
or all of this tax if you can show that any shortfall in the amount
of distributions was due to reasonable error and you are taking
reasonable steps to remedy the shortfall. If you believe you
qualify for this relief, attach a statement of explanation and file
Form 5329 as follows.
1. Complete lines 52 and 53 as instructed.
2. Enter “RC” and the amount of the shortfall you want
waived in parentheses on the dotted line next to line 54. Subtract
this amount from the total shortfall you figured without regard to
the waiver, and enter the result on line 54.
3. Complete line 55 as instructed. You must pay any tax due
that is reported on line 55.