Yes, if all the tiles in the same template position have 100% probability, there is an equal chance for all of them to show up.
As for the issue, can you open a bug in out tracker? I might have found and fixed a very similar issue but not quite exactly the one you are experiencing.
Please make sure to provide all the steps that reproduce the issue, that is the fastest way to get it sorted.
Thanks!
Just published the bug report. This is my first bug report using github, I hope I did it right.
It's pretty straight forward. You just need to create the object, create a new brush or use the default brush and set some tiles. Clone the object and see the brush configuration missing
github.com/Scirra/Construct-3-bugs/issues/4276