No solution other than keep track of the folders you create and save to the opposite one...until DISH fixes the problem and sends an update.
I think you may have the same or a related issue with the Sling and folders like I do. A little over a week ago I upgraded to 1 Hopper, 1 Sling Hopper (HwS) and 1 Joey. The non-Sling Hopper and Joey run like a champ so far. The HwS is a pain at times. Last week was rough for it with funky satellite signal loss (when there was none), problems with watching PTAT shows recorded on the regular Hopper, etc... During normal watching the HwS runs pretty good so far.
I did start to notice that when I tried to save recordings to a folder that's when the fun started. On the regular Hopper in the bedroom we only have two folders, a folder for my wife and one for me. On the HwS I made the folders: Concerts, Dad, Jacqui and Movies. When I try to save or move a recording on the HwS a lot of times the slot where the folder name should show is blank. Or, the list starts with Dad then a blank, then Jacqui and Movies. If I save to the slot that says "Dad" it really saves to Concerts. The reason is that while the screen shows the weird order, they really are in alphabetical order. I just have to remember that the first slot is Concerts, second, Dad and so on.
The display will show the proper folder name after I select one, but for the first few times I selected Dad, saved without looking at the folders selection and thought my recording was lost. Until I found it in Concerts. When I figured out the problem I saved to the blank slot and they were in the Dad folder.
What's odd is that I know I've done this before from the HwS where I've switched to the recordings on the bedroom Hopper and saved a recording to my "Jim" folder on the bedroom Hopper. But now (from the HwS) when I try to save a recording from PTAT to one of the two folders on the bedroom Hopper I see the HwS folders and NOT the other Hopper's two folders. I should see the bedroom Hopper's folder list since that is where I am saving the recordings (because you can't move a recording from one Hopper to another...yet).
See photos.