So I noticed something playing the "bottoms up," custom map and I couldn't quite explain it. Basically because I don't really have good strategy my tactic for most maps is just build a giant reactor farm and enough Launchers to outpace the emitters. Because this map has a whole lot of emitters that means I end up building way to many launchers and for some reason even though I have enough energy available and all my techs are upgraded all the way the launchers end up running out of energy and inevitably I loose. I wondered if there was some kind of cap on the number of packets the ship can send out at any time regardless of the amount of energy available.
Yes. The ship can send no more than 60 packets, unless you have crystal ore in reserve. If you do have crystal ore, then that limit can be exceeded for as long as you have crystal ore. FOr instance, if you have 1 crystal ore, and can generate 100 energy, you will be able to output 100 energy indefinitely. If you output 101 energy, then as soon as your reserve is depleted and you draw down that 1 crystal energy, you will fall back to output 60.
The good news is that 60 is more than sufficient on the map you refer to.