I just went through this myself, thinking I knew what I was doing, and discovered every way to go wrong.
First, if you're going to flip your pieces 180 to do the second row of holes, your pieces need to be an exact multiple of 32mm long. Mine were off by 1mm which caused a 1mm misalignment between the rows.
Second, the router bit needs to be exactly centered on the plate. Mine was off by a 2mm, causing a 4mm misalignment between the rows. Also, my plate, which came with the 584100 LR 32 set, doesn't fit my 1400 router

. Even when the indexing tab is right up against the base the mandrel is ~2mm away from the center of the hole. It doesn't matter that much if the misalignment is perpendicular to the row of holes, your rows will just end up closer together or farther apart. If it's in the direction of the row then your holes will end up misaligned by 2x the bit misalignment.
Third, you have to pick the right set of pins on the alignment stop. That is, when you position the edge of your board along the length of the rail, you need to choose the appropriate set of pins to get the edge to line up either with the center of a hole or halfway between them.
After wasting a few pieces I found that I could more easily avoid mistakes by checking, once everything was clamped and ready to go, that each side of the board was exactly centered in the middle of a hole in the guide rail. With that done I then cut the first hole for one row, flipped the board and did the last hole for the second row. I verified that the two holes lined up before cutting the rest of the row.
Note that you can save yourself a lot of alignment hassles by simply not flipping the board 180. If you just slide the board farther in or out to do the second row, and index off the same edge of the board for both rows of holes, then it doesn't matter what length the booard is, whether the bit is centered, or anything else.
Hope that helps.
--Niall