I'm not sure which program is at fault, but I noticed a problem since I installed mp3tag 2.39n.
If I add cover art to a Flac file with 2.39n and then open the file in Winamp 5.51 or 5.52 the art is not displayed or even shows as existing when I use the Winamp view file info. However, Flac files with artwork from older mp3tag versions (2.39l definitely) appear fine in Winamp.
I had this problem on two different computers. One with Winamp 5.51 and one with 5.52. One computer was a fresh install of mp3tag 2.39n and the other was an install overtop of 2.39m. Both computers are using the latest FLAC builds, etc.
(I only add art to FLAC files in mp3tag and I do that by right-clicking the empty album cover space and clicking "add cover" and select a file, usually 500x500 or smaller)