As a point of reference my system doesn't show this problem with non-PTAT/Auto Hop recordings. I can start a recording on a Hopper, stop and pick up on one Joey, stop and pick up on the other Joey at the Hopper or Joey stop point, and then stop and pick up again at the Hopper with the option of picking up at the Hopper or either Joey location.
As for the PTAT shows its a different story. If I start a show on the Hopper and watch the whole thing Auto Hop works great. However if I stop and try to resume from a Joey or the Hopper it returns to the start of the program and plays with Auto Hop disabled if I enable Auto Hop, but resumes at the right location if I disable Auto Hop (operates correctly).