Ok, i will try to explain it. First, an essential rule:
You don't need to use multi materials, use single materials instead.. and these materials must not be applied to Forest, but selected as parameters in the plugin. Following your example:
1) Create two standard materials, Tree1 and Tree2 in the material editor
2) Create a Forest object
2) Go to to "Modify" panel and open "Geometry" rollout. Each type of tree is defined in the "Geometry List", and each type have some parameters associated ("Properties" box). These parameters are: type of geometry (disabled, template, custom), width, height, z-offset, center, probability and MATERIAL.
3) Click "Material" button (below Probability parameter). On the material browser be sure that "Mtl Editor" is selected and pick your "Tree1" material.
4) Assign 60% to the probability parameter
5) Create a new type of tree, using the "Add" button below the "Geometry List"
6) Assign properties to the new item (it must be selected on the list): use "Material" button and pick "Tree2".
7) Set probability to 40%
That's all. You have created two types of trees, one with material "Tree1", prob. 60% and other using "Tree", prob. 40%. As you can see, for each one of them you may define other parameters as well: geometry, width, height and more.
We have not used any multi material or assigned a material to the object, Forest does it automatically. It collects all materials defined for each type of tree, and builds a multi material that assign to itself (this process is transparent to the user).
I know this is very different of how Forest 2 works, but the new system is much more flexible. As example, now you can use as custom mesh a tree that use multiple materials (trunk, leaves...). This was not possible in Forest 2, as each type of tree only may have a unique ID material. Or you can define multiple geometries in a single Forest object (tree1 as One Plane, tree2 as custom mesh...).
All these concepts are shown visually in the basic tutorial video.