Yes, iolite would refer to scanning back and forth in alternating directions to be "boustrophedon".
There can be a couple of reasons the edges of the image are not lining up: it could be a rounding issue in the horizontal coordinate; it could be that the horizontal coordinates of each line are indeed offset; or it could be some other effect. If you could send us a copy the experiment to the iolite support email, I can take a look and let you know what's going on, and fix any possible issues.
You can also process this sort of image in the "From Selections" mode, by selecting the "Boustrophedon" option in the Map Style dropdown menu. If you do process the image in this way, there is a "Justify" option in the Alignment dropdown menu that will align the starts and ends of each scanline. This does do some interpolation though, so it might be better to get the CellSpace issue sorted.