@pusen and I have spent maaaaany hours on this one! As I said, the fact that two sets of words decrypts into the same sentence, rules out almost every cryptographic method I know. I also noticed the lack of similarities between the sets. Word length, word classes, number of vocals, you name it.
A breakthrough was to find this list, which contains all 48 words:
https://en.wiktionary.org/wiki/Wiktionary:Frequency_lists/Contemporary_poetry
@pusen found a python script using this list, and this gave me a hexnumber easily translated to text. One step left, ROT13 - and the solution was found :)