There were also reports of Windows having problems with excess padding in FLAC files. See this topic for a slightly technical way of removing the padding
Yes, removal of padding (or at least resizing it to something that makes sense) is on my internal list of things to improve for Mp3tag. Until then, you can create this workaround using metaflac.exe (you can download it from the FLAC website , look for flac-1.3.2-win.zip).
In Mp3tag, define a user-defined tool via Options → Tools, and name it, e.g., FLAC remove padding, put the path to metaflac.exe and use the parameters
--remove --block-type=PADDING --dont-use-padding "%_path%"
If you want to …