I've already explained part of it, and this information is available at every major FFXI resource (copy/paste link in my sig for an example).
Spells cast by the automaton are grouped into categories of priority. What group is prioritized depends on maneuvers and the enemy's HP % (for instance, with the BLM head the automaton will always try to finish off a mob that's at very low HP with a nuke) or its own HP or the HP of you/your party members. Cures are prioritized by low HP and light maneuvers- light maneuvers with the damage gauge also raise the HP threshold for curing to make it easier to get it to cure. If not in the HP threshold but HP is not full, it will cast regen. if HP IS full, it should cast dia/dia II (if a dark maneuver is up, it should cast bio/bio II under those conditions, regardless of head)
Other maneuvers can prioritize enfeebles; the problem here, which I hope the other poster is alluding to, is the fact that you can't choose which enfeeble, except by having certain enfeebles on the mob already (which can't be done if the mob is immune, of course).
On BLM head, ice maneuvers prioritize (and generally enhance) nukes; however, the automaton will prioritize Drain if its HP is below 75% and Aspir/Aspir II if its MP is below 75% (In both cases, if the recast on those spells is up- besides the casting delay, the automaton has to wait the same amount of time as anyone else to cast spells)- this is the other sticking point among PUPs because while these spells are useful, there doesn't seem to be a way to override the aspir/drain priority.
As with the whm head, you can get dia/dia II with light maneuvers and you can prioritize Absorb-INT, Bio/Bio II and (I believe) blind) with dark maneuvers.
The use of the scanner causes the automaton to prioritize specific nukes based on what it thinks will land the best, but this often causes the automaton to cast absolutely nothing instead if it thinks nothing will land, either due to immunities/resistances or low magic skill on the automaton.
At any rate, the point that I was getting at is you can avoid some stupid things like the auto casting silence when it won't work by simply prioritizing something else instead with maneuvers or HP/MP conditions. If you prioritize curing/regen/dia, it won't cast silence. If you prioritize nuking or the automaton's HP/MP is low or you prioritize other dark magic, it won't cast silence.

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