Are you talking about ALL the FLAC tracks of certain albums not showing the bit depth, or just certain tracks? Find a track that isn't displaying bit depth, right-click on it, and choose "Send To: File Rescan"; after doing so and playing the file again, does it show bit depth? If not, can you post one of the files that should show 24-bit on an upload site somewhere so we can test to see what the problem might be?
It would also help to see the code tag line you are using in Track Information to show bit depth. Also, please confirm that you are using the latest version of MusicBee (3.2.6804+).