I've had this issue for a number of updates now.
If I insert a check box at the beginning of a paragraph and then hit a hard return in the same paragraph it will delete the last character in the paragraph.
Each additional hard return deletes an additional character.
My workaround is to hit all hard returns first, then add individual check boxes to each line.
It was better in the past, where I could take a single paragraph, add a single check box, and then hit multiple hard returns to automatically add check boxes.
The workaround requires repeated use of cmd+shift+T, which is an annoying key combination I can't change.
I could highlight multiple paragraphs at once and add a check box to all of them at once, but it usually ends up placing many more check boxes in random places.
I'd appreciate some attention from Evernote to their check box functionality, as I live by the check box.
Every day I copy massive email threads, paste them into Evernote, and then whittle them down into clean checklists to work from.
Their functionality has gotten wonkier over time and is starting to tax my process.