I use a normal M8N GPS and wheel encoders. This works really well, once the initial position is acquired, the rover does not drift over the map, like it sometimes did with GPS only.
Perhaps the wheel encoders somehow degrade the position the RTK GPS reports?
Or there might be some errors in your encoder setup. CPR needs to be set per wheel rotation, so you must take the gear ratio into account, depending on your setup. The wheel diameter must be correct and the wheel position too.
Those settings can not easily be verified by looking at logs, because they require meassurements at the rover.