I too have been tractored a moment after hitting antimatter spread on a borg cube that previously had me tractored. I have a theory on this:
Like scramble sensors, antimatter spread causes the enemy ships to cycle through friendly and enemy targets randomly. That does not make you immune to their targeting, it just means they also target other stuff too. If they were to randomly target you after you hit the spread, they could tractor you anyway and the active tractor beam is not dependent on maintaining target lock.
I've noticed AM spread being far far less effective than it was not so long ago. It was great using it against the hordes in fleet actions and so much fun against the crystal shards
I mainly used it as a tractor breaker, which it used to do absolutely reliably but right now it doesn't seem to like breaking them. Hell it isn't even confusing enemy sensors anymore, almost every ship I hit with it (within 5KM of me obviously) used to stop and target something else occasionally their allies but now they don't even stop they just keep on firing at me.
Yeah I noticed that, I broke a Tractor with the Heavy Graviton beam, because it was one of the few times it was possible, and it only let me go for a second or two.
Fortunately my PH came off cooldown, but it was annoying that the beam designed to be used against the Borg can't do much DPS, can't offline things for more than a few seconds and now won't even break Tractor Beams. It makes the MACO set a waste of time.
Note it's Damage is less than a Quantum Torpedo, they have an 8s cooldown it has 3 minutes.
Are you using saucer separation at the time that you try to use AM Spread? I have noticed that when I am in saucer separation mode (at least on the oddy, assume Gal-R is the same), the saucer will use AM spread. If there is a 30 second immunity and you then fire your AM Spread before the immunity expires, that might explain the lack of an effect. You may have to wait for the saucer's AM Spread immunity to wear off.