IDK what is the exact limit of sets to use, but yes, that's the reason
it happened to me years ago when i used many sets to show extra info in Xfire
i think when you use many sets in the config you break the limit of serverinfo string of the server,
and since the scoreboard info is always shown at the end of that string it gets truncated from it.
setcvar is just like set but for scripting only
also this is the difference between all the "sets"
Code:
set sets a cvar
seta sets a cvar and flags it as archive
sets sets a cvar and flags it as server info
setu sets a cvar and flags it as user info