From what I remember :
The “correct” format is to put all the check items on the first line of a given entry in the users file.
But, in FreeRADIUS 2.x, if you do, EAP-SIM (and probably all EAP types, though I did not test) will not work.
So you have to put them in the “reply” list (ie on multiple lines in the users file).
And ignore the warnings…
In FreeRADIUS 3.x, this has been fixed, so you can comply with the warning, and put all check items on first line of entry.