@ben2talk Thanks for your reply, indeed you are right the .cue file looks to be created for a .wav file, since it contains the "WAVE" tag at the end of the FILE value.
I want to point out for clarity that in Strawberry adding the .cue or the .flac file directly works fine as it is. (The problem happens when adding folders that contain a single flac / cue)
I don't really want to split the .flac in multiple files, still tried DeadBeef, and found our that in DeadBeef player adding the folders works just fine.
I also took a look at .cue format standard, and tried changing WAVE to FLAC, just in case : same outcome.