From the Actions section of the Listary Options, if I enable an item further down in the list (like "Edit with Vim" in the screenshot) and then click the move upward button, the selected checkbox does not move upwards with the entry.
Confirmed for 5.00.2410under Windows 10 x64
Thank you for reporting. I'll fix it.
Problem still exists in 5.00.2581.
This UI will be completely redesigned in Listary 6 so I didn't fix it in 2581.
That'll work just fine. Thanks for the great work.