Up until now I had been signing my apks with the following method:
jarsigner -verbose -sigalg SHA1withRSA -digestalg SHA1 -keystore {keystore-file} {apk-file} {key
The original answer can be found on the comments of the question, I am moving it here in order to mark the question as answered.
Although I am still not sure 100% of the details, the problem was the password I was using for my keystore contained special characters (* and !). After changing the password to an alphanumeric format, the problem was solved. So it seems like apksigner does not accept the same format for passwords than jarsigner.