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
I cannot vote/comment yet, but +1 for max's fix:
./apksigner sign --ks test.jks --ks-key-alias test --ks-pass pass:testtest --key-pass pass:testtest Test_Aligned.apk
Prefixing my passwords with "pass:" worked for me
--ks-pass pass:MyPassword --key-pass pass:MyPassword