Why don't you convert the WAV to FLAC with foobar2000 using flac.exe?
It sounds to me like you are trying to play the files incorrectly. Just drag your FLAC file into playlist and double click it to play it. There's no way the player would not give error if something is wrong and it also never plays different file than asked.
but are you saying to me that I cannot play a file through file-open file if it hasn´t been added to the playlist first?