I am using foobar2000 v0.9.3.1 and the Monkey's Audio decoder v2.1.1 component in Linux via the latest version of wine to convert a few of the ape/cue albums that I have to flac-files-per-song for playback on my Rockbox device. It works well most of the time, but for a song here and there a few clicks end up in the first few seconds of the flac file. Using foobar2000 to convert to wav instead of flac, then using flac on the command line on the wavs eliminates this problem, but it adds another step which takes time.

Has anyone else experienced clicks in their converted files? Thanks!