I don't think so. There has to be some sort of delay before the Phoenicia jumps out. When it gets hit head-on by the Sathanas, it's hull drops like crazy, doesn't it? It probably dropped so fast that, in that moment between the point where the event-true delay is called and the ship-depart order is given, the Phoenicia took a bit more damage.
There's an event that throws a ship-guardian on the Phoenicia after the Sathanas opens fire. Problem is, the event is set to trigger when the Phoenicia's hull reaches a very specific value (the mission's author used an equal-to operator instead of a less-than operator) which is occasionally skipped right over because of the rate that three to four of the Sathanas' beams can pump out damage. As a result, sometimes the Phoencia lives, and sometimes it dies.
I don't think it has anything to do with the framerate. However, if the Sathanas fires its beams such that the Phoenicia takes so much damage that it actually skips the 4% hull integrity mark...you get a toast Hecate. I've experienced this before when I was making a remake of Slaying Ravana. In my mission, I set the events such that a Demon-class destroyer would jump in when the hull integrity of the Ravana is exactly 42%. However, if the Ravana gets hit by a Cyclops at the right time, such that the Ravana's hull drops from, say, 43% to 39% in a single hit, the arrival cue event will always remain false and the Demon will not jump in at all.