I print and cut metallic all the time and I gave up on the auto registration marks a long time ago. Even with all of the various tricks, it was a crap shoot when it came to reading them. I'm using Flexi and cutting with a Graphtec FC-7000. When dealing with metallic media I always specify using four-point manual marks and use the plotter's build in light pointer to manually locate all four marks. It takes a bit more time than using automatic mark sensing and, if you're not careful, it won't be as accurate but it works each time, ever time.
Realizing that the cutting accuracy is dependent upon my less than ideal eyesight, I always try to design the jobs such that a little bit of cutting inaccuracy won't hurt anything. Like not cutting to the edge of narrow outlines. I figure that I can get the registration within 1/64" and I don't want any error worse than 1 part in 10 so I avoid having outlines and/or objects less than .16", or so, that are on the cut path.
I'm fascinated by the effects possible printing on metallic silver. !'ve been printing a lightly variegated gold pattern with a bump map that from a few feet away cannot be distinguished from real gold leaf.
As for media I've gravitated to 3M 180C Light Silver and Avery Ultra Metallic. I've tried other silver metallic media but these seem to be the lightest. Knowing just how to adjust your colors to compensate for the white point [or lack thereof] of the silver media is key to using these vinyls.