Ok, so I broke hacking again. Several ways.
*note: The CounterHacking logfile is still using LF rather than CRLF in a bunch of places, making it hard to read sometimes... could this get fixed?
First - I have at least one saved game that crashes when I try to load. It takes a LONG time to load, then I get lots of ClientReceivingData errors followed by a bunch of AILoopErrors, followed by my Home Command Station blowing up and instantly losing. I suspect this is just because of the huge amount of stuff I had sitting around (very late-game save) during the version transition.
Second, the tooltip for the Hacking Progress is a bit messed up: The number listed for "Next SuperTerminal Tick" cost doubles every tick, and quickly overflows (showing '0' afterwards). However, this is a display bug only, as the correct value is being added to the "Spent" total.
Third, as soon as the Hacking Progress becomes negative, the SuperTerminal started ticking every second, rather than every 15 seconds.
Fourth, things got crazy - really crazy - for about 30 seconds as the negative Hacking piled up. Then, well, here's a sample of the CounterHacking log file:
7/3/2013 3:47:02 PM (7.002) 19:55:49 Counter-Superterminal-hack Spawn
spawnStrength = TotalNumberOfSuperTerminalTicks * 4 = 756
BaseHackingAntagonism = AIProgressionLevelEffective = 149
HackingProgressEarned = AIProgressionLevelTotal = 599
ShipDesignHackingCost = 50 for the first hack + 100 for the second hack + 200 for the third, etc = 150
KnowledgeHackingCost = 30 for the first planet's worth of K + 60 for the second + 120 for the third, etc = 0
SuperterminalHackingCost = 20 for the first planet's worth of AIP + 40 for the second + 80 for the third, etc = 14827.5
FabricatorHackingCost = 20 for the first hack + 40 for the second hack + 80 for the third, etc = 0
AdvancedConstructorHackingCost = 100 for the first hack if done + 200 for the second hack if done = 0
HackingProgress = -14378.5
minimumBaseAntagonism = -hackingProgress = 14378.5
BaseHackingAntagonism = Max(BaseHackingAntagonism,minimumBaseAntagonism) = 14378.5
negativeHackingProgressMultiplier = Mat.One + ( minimumBaseAntagonism / 10 ) = 1438.85
BaseHackingAntagonism = BaseHackingAntagonism * negativeHackingProgressMultiplier = 20688502.62
multiplierForSuperterminalHackResponseSpawn = 1 + (totalHackingAntagonism/200) = 103443.51
spawnStrength *= hackingMultiplier = 78203293.38
maximumNumberOfWildRollsForSuperterminalHackSpawn = 1 + (totalHackingAntagonism/100) = 206886
...
...
...
wild-roll:InnocuousRoll, spawnStrength = 2028143761413.21
multiplied by 0.93 to reduce recharge to 14, spawnStrength = -159487527862.87
With a base spawn strength of 80,000,000 and over 200,000 wild rolls, it quickly overflowed the strength, resulting in a negative value, aka "No Spawn". Oddly, after a while it went back to normal spawns every 15 seconds, with overflow no-spawns every other second, and then got OutOfMemoryExceptions starting about -20,000 Hacking Progress.