The official GPG binary from "c:\Program Files (x86)\GnuPG\bin\gpg.exe" does not exhibit this problem. I will report it to the msys2 folks.

Yes, it is the msys2 build of gpg, installed using the standard msys2 methods. The pwd in my example was from msys2 zsh.
I reproduced the error running under msys2 zsh and in Powershell.
If I understand your response correctly, you are saying this will not be fixed in gnupg itself? I can report it to the cygwin/msys2 folks of course, if you think that is best. But I still suspect the root cause is in gnupg, probably in homedir.c or the code that makes an absolute path from a relative one.
I will retest with the official gpg4win and let you know the results.

In D600#6448, @ikloecker wrote:

$ man getdents64

getdents64()
    The  original  Linux getdents() system call did not handle large filesystems and large file offsets.  Consequently, Linux 2.4
    added getdents64(), with wider types for the d_ino and d_off fields.  In addition, getdents64() supports an  explicit  d_type
    field.

    The  getdents64()  system call is like getdents(), except that its second argument is a pointer to a buffer containing struc‐
    tures of the following type:

        struct linux_dirent64 {
            ino64_t        d_ino;    /* 64-bit inode number */
            off64_t        d_off;    /* 64-bit offset to next structure */
            unsigned short d_reclen; /* Size of this dirent */
            unsigned char  d_type;   /* File type */
            char           d_name[]; /* Filename (null-terminated) */
        };

Go ahead and split it of, then. And setting a key to disabled in Kleopatra itself is not that urgent that it has to be in vsd33.

I think Kleopatra now respects the "disabled" state of OpenPGP certificates. I don't remember the outcome of our discussion about allowing to disable OpenPGP certificates from Kleopatra, but I think this should be split out of this ticket.

Tobias should have addressed all points (except using ISO format for dates which we won't change in Kleopatra).

$ man getdents64

getdents64()
    The  original  Linux getdents() system call did not handle large filesystems and large file offsets.  Consequently, Linux 2.4
    added getdents64(), with wider types for the d_ino and d_off fields.  In addition, getdents64() supports an  explicit  d_type
    field.

In D600#6445, @gniibe wrote:

If it is intentional change by musl (requiring some changes by an application), we can use __ino64_t_defined and __off64_t_defined macro to see if those types are defined or not.

Verified in pinentry-1.3.0.

Fixed in gpgme 1.21.0.

Fixed in pinentry 1.3.0.

pwd is not a standard Windows command. It is availabe in powershell but there I get

Fixed in 2.4.4.

If it is intentional change by musl (requiring some changes by an application), we can use __ino64_t_defined and __off64_t_defined macro to see if those types are defined or not.

I think so. We did not submit a modules for recertification with these changes, but we do not plan this in close future so you can consider it completed.

Can we close this?