I had researched this a few years ago and my conclusion is that ProSeries does it correctly.  The non-deductible expenses are prorated when there is not enough Basis.

Offhand, I can't remember the Regulation or whatever that dictates that, but I do remember that my conclusion is that prorating it is correct.

As a side note, although I realize many ProSeries users use Form 6198 for this purpose, it is NOT correct to file Form 6198, as limitations for"At Risk" is different limitation than "Basis" (although the calculations are the same).