If you're printing on white media the marks should be fine without any need to augment them with Sharpies, snot, or whatever. Redrawing marks by hand is tricky at best, usually silly, and always inaccurate. If you just have to get something contour cut and your auto sensing tackle is not working reliably, use the manual 4-point marks and, if your rig has the light pointer use it it locate them. If not, it's not rocket science to just use the tip of the blade. Assuming your eyesight is adequate. This method is slow but if you take care, it's sufficiently accurate for most jobs. It's also a better way to do contour cutting on media that isn't friendly to sensing. It beats the hell out of the endless parlor tricks that people try to fool the sensing tackle.
I would assume that you're using the Graphtec type 2 marks, by far the most common choice. Are you starting by placing the blade holder inside the first mark close to the corner and then setting the origin to this point before you start? If you don't it's likely the plotter won't find anything.
I further assume that you're set up to use the large ~1" marks. The smaller marks from days gone bye can be a b!tch.
If it reads the first mark but has trouble with any of the others it's usually because the media is skewed too much or, more rarely, the feed compensation on the printer, the plotter, and the software is wildly divergent. I.e. is what the software thinks is 1 foot pretty much what the printer and the plotter think is 1 foot? The only leeway you have in this is the size of the mark.
