A bit more info.
Matte and Fill have to be same resolution. No surprise there.
Seems to be some issues with smoke containers. They do not seem to be compatible with containers created in lustre expressly for mattes.
If you have a clip in lustre, create a matte container by holding control before selecting Ctnr. After the matte container has been created add one clip or more into the container by holding down control as you drag the clip over the container and release. This will automatically change the clip to secondary and add it to the container.
R or G or B must be enabled when selecting the matte. It helps to show matte (M) in order to make sure you know which matte has been selected. Select which matte you are using by select S, V1, V2, etc next to Matte.
If in the container, you press the middle mouse button when selecting the (S) secondary layer, you will crash the program. Nice.