|I would guess that it's more about sizing than your covers wearing out. I usually found that leaks meant it was time to move up a size, even if the cover seemed to have room left in it.
That being said, it's probably both things you note--as you daughter is going more at once (probably a good sign as she moved toward PTing, right?), you might want to put a liner in each diaper; even though she might not truly need the absorbancy total, she might need it to cope with the sudden release.
You will probably need L covers anyway, but do you have enough liners that you could do a test day with liners in each diaper and a L cover to see if the combo makes the difference?