Are you using anything like a barrier cream which could have coated the liners? This might make them repel liquid, it certainly sounds like the fleece is not letting the pee through to the nappy if baby has wetter skin that without. Might be worth strip washing them, shouldn't take long with liners? A good scrub with a nail brush and some washing up liquid then a mega rinse session in wash machine should remove any creams, or manufacturing residue or similar which may be on them.
If it isn't that then maybe they are just duff fleece? Like a lot of the PP I have never had problems with fleece liners, no matter what way they were put on and even with fleece on fleece.