I had the same problem on my system, and fixed it coincidentally while packaging the flatpak.
On Linux, the “mailsync” shell script calls the “mailsync.bin” binary. When closing, the shell process is terminated, leaving the mailsync process hanging, which in turn causes it to behave buggy.
In the latest flatpak, i do not use this shell script, instead “mailsync” is directly the binary. Since then closing works as expected.
@bengotow using exec to call “mailsync.bin” will probably fix it for other distribution methods too, as the shell process will then get replaced by the mailsync process.
Will try once 1.19.1 reaches Flathub.
It already did and should work because of the reasons above. It just shows up as 1.19.0 because of The 1.19.1 release is incomplete.