Spent an hour with tech support supervisor today asking this question, and an hour last week as well.  Nobody seems to know, even to understand what the issues are.  Am thinking you could trick the program by inputting all as timely paid and get around the penalty portion for those payments, but then the dates shown on 2210 will not line up with dates received by IRS.  Hopefully Lacerte will notice this and other inquiries and come up with an update to solve the calculation.