Wow, I've never seen so many glitches at once. Your game seemed almost like it was overloaded: first, the detonation animations for all your weapons disappeared about the time you destroyed the mainframe panels; second, a number of enemies that should've teleported in never showed up, simply making a noise as if they're going to teleport in, but they don't. I've never seen this problem before, and honestly I can't say why it would've happened.
Also, you need to get rid of the Tick and S'pht'Kr sprites in your HD Monsters plugin, because the Ticks are not actually Ticks anymore - they're helpful floating cyborgs with fire blasters (though the red and green variants don't seem so friendly).
Vale,
Perseus