You need to build the array in your loop, and then call handsontable afterwards. Here is a first-cut of restructuring the code. You will probably still need to tweak it to get what you want:
var data = [["", "Date", "Invoice amount", "Interest rate",
"Interest amount", "Amortization", "Capital balance"]];
for(var i = 0; i < PmtPeriods; i++) {
data.push(
[i + 1, StartDate, 2000, IntRate, PV*IntRate/360*30, 1500, 100000]);
}
$("#dataTable").handsontable({
data: data,
startRows: 10,
startCols: 7
});