Hey Frederik,
This is actually unavoidable for several long technical reasons. But the gist of it is, when a .NET app functions as both a GUI and a commandline app you get weird quirks like this.
We used to have a fix where a new prompt would appear below "Updates built successfully", but this caused several problems on build servers that run under the System account. Thus we had to remove the "fix" that actually broke more than it fixed.
To sum up, we're aware of the problem, but it won't be fixed soon. In the future we will have a separate commandline-only update builder that companies can deploy on their build servers, and remove the commandline building from wyBuild.exe completely.
Sorry for the confusion.