One possible explanation is that the asset was inherited.  Some brokerages are good at updating the basis with the stepped up basis, but the date would be recorded as the transfer-in date.  Inherited properties are long-term assets regardless of the holding period between the inheritance and sale date.  If this was the case I would check the "inherited property with stepped up basis" box on Lacerte and make the acquisition date marked "INHERITED".

I would ask client if this was the case.  If NOT, I would NOT waste time fining out why the grouping in long term happened., and just force it to be long term as reported and make the acquisition date "VARIOUS". 

As for your question, I don't have actual knowledge if it matters.  Unlike Bob.