It's also broken in Total Commander, maybe you are using the same libs... (?)
You could also look for the official libs instead of 3rd party support, which would let you (or the user) replace them in the future easily.
https://xiph.org/flac/api/Or the cue tools libs, which include Flac, Lame for Mp3, Wavpack, Ape, ... already compiled and ready to use (64 & 32 bit dlls)
https://sourceforge.net/p/cuetoolsnet/code/ci/default/tree/http://www.cuetools.net/wiki/CUETools_DownloadPD: Also some of these formats (Flac for ex.) are capable of storing MD5 signatures related only to the musical content and not the "tags", known as Flac Fingerprint Files. I work with them regularly.
Using the official libs it would not be difficult to use multicommander as a gui for them via commands and perform audio file checksums wich would be great. Or even integrated in the file checksum plugin.
The only program who does that is called "The trader's little helper" but is totally outdated. I now use my own set of scripts to do it but it would be a really interesting option that could attract many users in the future from Audio Forums.