What version are you running? There were certain versions where "FLAC" was not available under file associations (yet another bug that benn found, if i recall correctly). Please download and install the latest version available here, v.179. I just loaded it and FLAC is available under file associations.
Note: if you've already imported FLACs and can't find them, they are likely listed as "documents", which is what MC does with file formats it doesn't recognize as audio, images, or video. You'll have to delete them from your library (but NOT your disk), and re-import them.