I think I understand the problem. Perhaps I should know an easy answer, but I don't.
Some patterns have to have stitches added at the beginning, the end or both to get them to turn out right. Often a stitch will give a repeat and a "+" number. Like "this pattern is a multiple of 12+3". I don't know how the patterns work out every time in those kinds of cases. Maybe you could do a small swatch of the multiple part done twice or three times and see what happens. You may find you need to add 3 only at the beginning to get it to work, but perhaps that is not a hard and fast rule. Some patterns are pretty complex.
Not a good answer, but I at least know what you are talking about.
Maybe someone with greater powers of observation will have figured out how all this stuff works out all the time. Lets see if we get more input.