I had a similar problem with my connex. Stratasys changed the encoder and it didn’t help, but one term stratasys used to describe this problem was “data shifting”, so it at least sounds to me more like a software issue. They also had me replace the ethernet cable that runs between the printer computer and print head, but that didnt help either.
I’ve found that restarting both computers before every print job seems to keep the problem at bay–my guess is that one of the two computers is lagging and causing a problem with job packing or causing a delay in how job instructions are sent to the printer–I assume the restart clears something, and that gets rid of the problem for at least one job.
It is a really weird thing, and it will print the same job with the same type of offset “shadows” in the exact same place until I’ve restarted both computers and repacked the job. Because it is consistent in this way, I’m leaning more towards a job packing problem, but just repacking doesn’t fix it, it has to be a repack after a computer restart.