Sorry for the delay. Perhaps I don't understand your setup, but it seems to be working fine here.
I am using a similar setup to yours. Multiple decals projected onto multiple boxes. Multimap in "Object GBuffer ID" mode. Each Box object (not Decal object!) has a different ID assigned using right click > object properties > object gbuffer id.
As you can see, different opacity masks are used on different boxes, depending on their ID.
Also, if you project a single decal onto multiple boxes with different IDs, that single decal will use multiple opacity masks (as expected).
I am using Corona 10 RC1 but will check if the same thing happens in V9.
Update: it is working in V9 as well. I will need to know more about your setup to understand what seems to be the issue.