I'm one of these strange persons who don't use the media library and instead browse through their chaotic file structures to play/enqueue an artist/album from the context menu. Additionally most of my albums are ripped with EAC, including a m3u and cue sheet - I ripped each track individually though (not just one flac/wavpack/... file per album).
With foobar 0.9.5.3 I encountered a small issue that each file is sometimes (strangely not always) enqueued twice in the playlist - one time the normal flac file and one time via the cue sheet. (see here)

I don't think it's the same problem already covered here because this issue only came up with v0.9.5.3.
Is there some way to fix this? And no, I don't want to rename the cue sheet whatsoever.

No one else experiencing this problem?

Does maybe changing the file type associations help?
(Preferences-> File Types)

I think maybe you're going to have to show us something reproducible for us to be able to help you.