the issue is "walking"
The biscuit joiner cutter enters the work by registering the platform against the piece to stabilize it. A router also has a base, but it mist not tip in the process or your slot will get too wide. Finally, the router will tend to walk in the direction of the rotation and the slot will become elongated. The slot cutters are a certain radius and thickness that may or may not suit the size and thickness of the biscuits commercially available.
The base on my joiner has little spikes or prongs that can protrude into the work to keep it from walking when the cutter is pushed into the work.
The answer to your question will only be as detailed and specific as the question is detailed and specific. Good questions also include a sketch or a photo that illustrates your issue. (:< D)