Several suggestions for things to review, as I've had no problem with the form and its usage of stock and debt basis info, so I have no reason to think the form is faulty:
(1) The statement "These are active losses so they should be allowed" is not correct - regardless of how much the active loss is, you are limited to the total of stock and debt basis...period!
(2) There are no negative numbers anywhere on the form, so if things are coming up negative the underlying information has been entered incorrectly - I think that is the underlying problem.
(3) The total in line 47d should be reflective of your total debt basis from line 29, OR whatever part of your line 29 debt basis is needed to cover remaining losses in excess of your stock basis.
From your discussion, it seems clear that you understand that first "stock basis" is used to cover the loss; once your stock basis is exhausted (reduced to 0), next debt basis is applied, assuming there is still more loss to be offset. Once debt basis is exhausted (reduced to zero), no further losses can be deducted and they are carried forward to next year.
(4) If, for example, stock basis is insufficient to cover your loss, then start allocating debt basis to cover it, but in no case can 47d (which should be a POSITIVE number in that form) be greater than 29 - maybe it's less than line 29 because you didn't need to cover remaining losses in excess your debt basis.
(5) Whatever part of debt basis is used to cover losses (line 47d) is then subtracted in line 30 from your starting basis in line 29, resulting in whatever carryover debt basis you might have - again, it seems you've fully understood this, and no, that line 31 number can never be less than 0.
