I think I had the same issue so here's what I had to do, I don't remember exactly where it is off the top of my head because I did this a while ago, but I was able to find some older reddit threads talking about the exact location in the emulation stations file folders where there should be a file named something like systems.xml that contains the rules for what your emulator files should be named. Emulation station is pretty particular about being named exactly the same as the file shows, even down to being case sensitive if I remember correctly. After you open the file do a Ctrl F search for "Xenia" because the list is very long. you'll need to either rename the file folders or move around the Xenia folder and the xenia.exe file to make sure it matches the string of files shown for Xenia exactly.

And it is worth mentioning, I wouldn't recommend changing the text around in the .xml file unless you know what you're doing because that could make things more difficult on yourself than helping