It only shouldnt in this version, i assume he has an older version where he unlokced that vanilla foxtrot and now he has updated to the latest version, but it doesnt mean anything.
The only source of problem i can see is that he he has non intalled mods below XCE, but i automatically assumed he knows what he is doing, that is if the modloader asks if he can sort the mods you have to click "No". Its not optimal to
have non installed versions of anything. The modloader is a frail construct, bugging out most of the time. Use it in the right way.
have mods below XCE. XCE IS NOT A MOD, ITS THE GAME ITSELF. Although it appears in the mod list as another mod. This can lead to trouble all along the way.
Read the text.
If you have any subsribed mods on steam either
Install and deactivate them or
Unsubscribe and delete the zip in your mods/... folder as well as the mod folders.