The attachment I included in the original report: "proguardoutput", is a text file that has the configuration at the beginning, and after that (separated with some blank lines and a line of equal signs) comes the log.
The configuration file is generated by a build tool, nevertheless I've inspected it myself and played with it, and I can run proguard directly with that configuration file and I still observe this behaviour.
Errata (because I can't seem to be able to edit the original post): (it ends up taking like 30 minutes, instead of ~40. I meant 40 seconds. The classes that are being kept, all belong to some scala libraries I have in the classpath, though only some classes of some libraires are being kept (it's not even consistent) I meant it doens't keep the library in full, but only some classes, not that the resulting classes change between runs.
Unrelated classes are being kept.