Unlike previous versions, Uninstaller 1.12 use a different behavior to do its job.
The new uninstall process:

1) Select your main disc/folder and do just "Save" (this create/update the saved state)
2) Install your new app, use it, create documents, etc...
3) Do "Compare" (this create the current state and compare it to the saved state)

Now Uninstaller show you New, Modified and Removed items since 1)

4) Review New items and delete unwanted files.

That's all.

Optionally, you can update the saved state by doing "Save" again after 4) if you consider to compare later your disc/folder from this point.