Code:
STEAMSTATS: SECURITY CHECK FAILED - ../System/LethalGoo.u
STEAMSTATS: SECURITY CHECK FAILED - ../System/DoomPawnsKF.u
STEAMSTATS: SECURITY CHECK FAILED - ../System/2Dview.u
...so no Perks for this server, what kind of override you are using?


I really don't know what to tell you man but I just tested it again.
Whitelisted map as SS, did 3 headshots, headshot count went up, map voted to Arcade-Mission, died instantly, map voted to Ganja Farm, did 4 headshots, headshot count went up. I didn't do nor change anything from WebAdmin, did everything as if a real player was playing.
Hell the server itself shows up as Perks Enabled and VAC Secured in the server browser.
AFAIK, Perks being enabled vary according to maps and mutators not to the server itself. If the server is playing a whitelisted map with no additional non-whitelisted stuff in that map, then perks should be going up as normal.
While the map may be using DOOM system files, the gametype for it is still regular KF.
I don't know what the explanation is as I'm not an expert in custom KF content or running servers, I'm just telling you like it is.