Hello Slau and Ignasi!
Here my last update...
It makes no difference how the selection of the files is done.
Both, the Finder and the search dialog work the same.
The problem is, that the integrated encode function only accepts a maximum of 1000 files.
Selecting a single file more will deactivate the menu item "Encode Selected Audio Files".
I double checked this on different hardware platforms.
So I finally used an audio convert app for that.
Best! / Martin