Hard to say without knowing what you are doing exactly. But I don't think that the number of calculation influences Mathcad's results. I rather guess its an error in the way you do the calculations or read in the data which by chance just shows in certain situations. I guess that not all calculations are wrong but just some beginning from a certain point!?
For example if you read in the data from your excel sheets and you do not initialize the matrix you read it in, ther may be values from a prior read be left because the new matrix should be smaller because you read less data.