One possibility is that the different DEs are using different font files. That seems like quite a stretch, but we can bother to go down that lane if you wish. You will need to install
strace. Because it is a command line utility, it might not appear in a graphical package manager. You should investigate using apt-get or yum or zypper or the other appropriate package manager for your distribution of Linux. The command will probably simply be
sudo apt-get install strace.
Once you have strace, run the program with strace in a terminal.
$ strace /opt/FreeFileSync/FreeFileSync 2>&1 | grep -iE 'font'
Strace will show us the system calls FreeFileSync makes, that is, the commands it tells the kernel to do. I use strace when I want to see what files the program opens. In this case, we only care about any font files it looks for, so we are just searching (with grep) for "font." The 2 greater than-ampersand 1 sends the output of strace to the pipe so that grep can actually search its contents. This bit moves standard error (given a file number of 2 by default) to the same output as standard output (file number, or file descriptor 1), and standard output is what gets piped to the next program, which is grep.
Run this command inside each DE, and maybe perhaps we can learn if the fonts it loads are coming from different places.
When I run this program with strace, I see this entry (among others)
openat(AT_FDCWD, "/usr/share/fonts/truetype/liberation2/LiberationSans-Regular.ttf", O_RDONLY) = 7
Perhaps you have configured your MATE environment to use an italic font by default for everything? I have a LiberationSans-Italic.ttf but my FreeFileSync did not try to load it.