when you zoom in to see discrepancies on a rectangle that small... you are literally splitting hairs. just cut them, they are fine, you could never tell by eye anyway. Unless you are working with thousandths of an inch, you are worrying too much about it.
Screen displays can play with things & the look of 2 lines perfectly aligned at one zoom level, & then lookign like they are not aligned at a different zoom level is a common occurance, so a big part of not losing your mind over it, is to quit worrying about it.
Freds solution will give you perfectly matched squares. It will take longer to cut... but far less time then what was spent in posting here, so it is a good solution. HSG's idea is what I have done & will speed up the cut time greatly. Even if you dont use a "step & repeat" function of your software, it should be easy to set up long lines that make up your grid with no double cutting. If you zoom in when you set them up, your level of accuracy should easily exceed anything visible to the eye, even if not as computer-perfect as Fred's approach.
In very long cuts, many plotters I've used will pull through 8 feet (or whatever) of vinyl while cutting a line... then it will send back the 8 feet without cutting so it can go to the next line... all this movement increases the chance for a problem... (tracking, bunching, me stepping on, or rolling my chair over the vinyl
not to mention wasted time) so I would set up a zig zag deal that uses one continous line to create all the lines on the length of the vinyl. I would still use seperate lines for the shorter ones across the width of the roll, since these do not result in as much of the wasted motion or time. (at each end you can leave off the last line to avoid "double cuts" but I just cut it & the double lines don't go through the liner on my plotter... they may score too deep for easy weeding of letters, but would not hurt in this instance.