I think I have found the root cause of the issue, my dad's ereader was showing that odd behaviour, I did two things at once (not the smartest troubleshooting technique but I had spent too much time trying to resolve it). I believe the cause of the problem is that some of the books had two formats (EPUB and ORIGINAL_EPUB) and I think that was confusing the ereader... I deleted the old formats in calibre (clicking on edit metadata and then deleting the old version at the right hand side of the window), just in case I deleted all the books from the eReader, manually deleted the collections and then reload all the books, problem solved.
The other thing I did was changing the way the tags are managed, setting it up to automatic (the option is under the device menu).
I hope it helps!