[gaeorn]

Lay hands and harm touch were abilities. I'd bet the hardcoded refresh for them was done before they were considered spells in the emu code. If you look at this excerpt from zone/features.h:

//Reuse times for various skills, here for convenience, in sec
//set to 0 to disable server side checking of timers.
enum {  //reuse times
        FeignDeathReuseTime = 9,
        SneakReuseTime = 7,
        HideReuseTime = 8,
        TauntReuseTime = 5,
        InstillDoubtReuseTime = 9,
        FishingReuseTime = 11,
        ForagingReuseTime = 50,
        MendReuseTime = 290,
        TrackingReuseTime = 9,
        BashReuseTime = 5,
        BackstabReuseTime = 9,
        KickReuseTime = 5,
        TailRakeReuseTime = 6,
        EagleStrikeReuseTime = 5,
        RoundKickReuseTime = 9,
        TigerClawReuseTime = 6,
        FlyingKickReuseTime = 7,
        SenseTrapsReuseTime = 9,
        DisarmTrapsReuseTime = 9,
        HarmTouchReuseTime = 4300,
        LayOnHandsReuseTime = 4300,
        FrenzyReuseTime = 10
};

you see that all abilities have their times hardcoded. Perhaps this can be changed. You'd have to check with someone more familiar with the applicable sections of code.

AA's have their refresh timers in the DB table aa_actions in the column reuse_time.