I'll chime in with similar Graphtec issues. We tried an FC5100, FC7100 and FC8000 before throwing in the towel and moving to a Summa S160D.
Same issues with Graphtec, they couldn't find registration marks to save their lives. The only way we could get even remotely repeatable results was to fabricate a plastic "hood" to cover the plotter to make it totally dark while it was searching for them. We also had to turn the lights out. This was on all three machines. Even then, it would not find about 1 in 10 marks. For comparison sake, in the 4 years since we've had our Summa, it's read tens of thousands of marks and to my knowledge has never ever missed a single one. We also had significant tracking issues on the Graphtecs on anything over 10-12', significant meaning we really could not contour cut anything over that. On our Summa, we regularly contour-cut 20-25' long prints and have successfully cut panels that were over 50' long with less than 1/4" side-to-side walking (which OPOS compensated for and the cut was perfect).
And on the subject of service, Graphtec was marginally helpful at best, they were responsive, albeit slow to respond, and they were never really able to offer any solutions. Summa's service on the other hand is considered by just about anyone who's ever dealt with them to be among the best in the industry, if not the absolute best. If you search around, these are issues that are very very common to these machines, I think I've actually talked to more Graphtec users that do have the problems than those that don't. Some lower-volume shops may be able to make due with the issues, but we run a tight ship and we can't be worried about whether a piece of equipment is going to decide to work right today or not. Graphtecs are not up to that task.