Compare a problematic file with a non-problematic one and see how they differ. It’s possible one file is a raw FLAC stream and the other is a FLAC stream in an OGG container.
ffmpeg’s handling of FLAC files sucks, and both types must be treated differently. Raw FLAC streams are what is commonly referred to as a FLAC file, FLAC in OGG is not that common.
It could also be an encoder problem with files produced by older/buggy encoders.