That has to create huge stresses on the windings. You wind up the flywheel, and then suddenly apply field current to activate the generator. They may be trying to ramp up field current slowly to reduce the stress. Some articles mention problems with a voltage regulator causing machine damage. Maybe the rotating machinery can't take a full-power turn-on.
Details on the system seem rather vague. Some published articles say there are four motor-generator-flywheel sets; others say only two. Isolating failed units electrically for maintenance is apparently difficult. Unclear why.
This unit "passed factory acceptance testing" in 2008.[1] These problems should have been discovered and fixed years ago. The manufacturer is Kato Engineering, part of Emerson Electric, acting as a subcontractor to General Atomic. They make a range of generators for various applications. So this is coming from a company with a long history of making generators. But generators are usually continuous-duty, not something that experiences shock loads like this flywheel rig. Apparently nobody insisted on some serious testing like running this thing through 50,000 cycles into a dummy load.
The linear motor of the catapult itself seems to be working OK.
The new arresting gear shouldn't have been a problem. That's mostly a paddles-in-water brake, something that's centuries old. How did that get screwed up?
Overall, the Ford series of carriers uses electricity for functions that, on other carriers, involve piping steam around. Most newer Naval ships are Diesel or gas turbine powered, and don't generate steam as a by-product. Nuclear plants do generate steam, which has been convenient for carrier catapults. The new British carrier series (if it gets built) is to be non-nuclear, and they want to use the EMALS launcher on some of the ships (maybe). That's part of a big mess - without a catapult, they have to buy the VTOL/STOL version of the F-35, which has its own problems.
There's an amusing book, "Ships, Machinery, and Mossbacks", by H.G. Bowen, from WWII. Bowen was a U.S. Navy engineering officer and eventually was in charge of most Naval propulsion systems during WWII. He was a real hard-ass on contractors, and often sent back large, expensive items like final drive gears back as rejects. Admiral Arleigh Burke ("31 knot Burke") wrote that his ships wouldn't have been able to go 31 knots without Bowen's work. When it really has to work, you need people like that who can say no.
[1] http://www.ga.com/emals-motor-generator-passes-acceptance-te...