I have exactly the same problem! I see no evidence here or elsewhere that. B&N is working on a solution, so I guess it is time to cancel my magazine subscriptions. . .
Yeah, it is pretty ridiculous that they have not fixed this issue, and it would make sense that they would see this during testing their software.
I found a really stupid and silly hack to get around this issue. I had to essentially, select the whatever issue that i could select, which in this case is the oldest issue on the overlaid thumbnails. Then i would tell it to archive it. I kept doing this for all 10+ issues I had overlaid, till finally, the latest issue was all that was left and selectable.
How do we get B&N to pay attention to this? Is there a support ticket that can be filed for this?
I have this problem as well! It makes the magazine portion of the app useless.
I'd love for B+N to fix this soon.