When I group by my group CAMERA and set registration "auto by CAMERA" the registration is done per filter and not by CAMERA. So in the following example all 6 stacks are registered differently so the first three can't be combined as is nor can the second three. WBPP seems to select a reference frame for each filter rather than each camera.
In this configuration, WBPP selects two reference frames, one for QHY11 peeking the frames with most stars amongst the first three groups, and one for QHY163M picking the frames with most stars amongst the last three.
At that point, the first three groups will align on a common frame, the last three on another one.
If this is not the case, could you upload the log file? I may check what happens.