1) I have definitely expected to get a skill shot and not received it; I always figured maybe I didn't hit the switch hard enough, but I think it is more likely what you are experiencing. Interesting! That's a code fix luckily..
I too am 100% sure I am hitting the skill shot targets but no reward. I think the timing of the lights is off as well.
2) The catapult (and to a lesser extent, the scoop coil) is HIGHLY dependent on consistent power from the wall. I am not sure if this is a normal thing for games and it's just more pronounced because of how precise the catapult needs to be, but I can validate that I experience some weirdness with the catapult as well, although not as extreme as you've seen -
For me, I have several games all on one circuit. When I have only Houdini turned on, the catapult nails the trunk consistently. When one or two other games are on, the catapult will start missing. The scoop will also behave strangely, having to try 2 and 3 times to get the ball out. Then when Houdini is the only one on, the ball will come FLYING out of the scoop.
I have the same power issues if another pin is on in the same room and on the same circuit breaker. Even if I tap the flippers when the ball launches with the other two pins off, the ball will drop short of the truck or hit the lip.
I emailed AP about that and they suggested a Variac unit:
ebay.com link: 1 3KW AC Voltage Regulator Variac Variable Transformer Metered 10 20Amp sale new
I'm considering this but for now I just make sure no one has the other two pins on in the same room when playing Houdini.
Just make sure you order the 1000W unit.