My bad.
I'm currently running the older version and was thinking about upgrading. I should have assumed that setting it to 0 would be the older method.
It actually doesn't say in the cfg about the effect of setting it to 0.
// Whether or not spawn protection is enabled.
// --
// Requires: sm_spawn_protection.smx
// Default: "1"
cssdm_spawn_protection "1"
Old CFG says
;Spawn protection stuff
;Time in seconds, 0=disabled
protection = 4
;type, 0=default (god mode for X seconds or until a shot is fired)
; 1=old style (500 HP for X seconds, then back to 100)
protection_type = 1
So i guess it not being there was enough to confound the Winky.