Update: Developer Wanam has confirmed on Twitter that the code responsible for the "boosting" behavior has been removed in the Android 4.4 ROMs for both the Note 3 and Galaxy S4.
— Wanam (@WanamXda) March 4, 2014
Months after the Galaxy S4 was released last year, allegations began surfacing from Anandtech that Samsung was essentially "gaming" its devices' CPU and GPU benchmark scores by leaving cores at "full throttle" when such benchmarking applications were launched. This allowed Samsung to achieve marginally higher scores in such tests than its rivals, and gave the Galaxy S4 and Note 3 the appearance of being a little quicker than a typical benchmarking environment would otherwise show them to be.
Benchmark-gate initially made waves in the tech press, but was rather quickly forgotten because, well, they're benchmarks - who really cares? Was the practice a bit deceptive - scummy, even? Sure. But there are no established rules for benchmarking, and really, if you're considering buying a phone based on a benchmark score, you probably need to evaluate your priorities.
Still, it was a dumb, dastardly thing to do, particularly considering the only people really paying close attention to benchmarks are rabid fanboys and in-depth technical reviewers like the team over at Anandtech. In short, it was a big PR gaff for an extremely small - practically nonexistent - payoff.
Samsung never really fully accepted responsibility for the practice, or admitted to any outright wrongdoing, but as this story goes to show: actions speak louder than words. The Android 4.4 updates to the Galaxy S4 and Note 3 don't just bring a healthy dose of KitKat, no no - Samsung's benchmark shenanigans have been eradicated according to tests conducted by arstechnica and Geekbench.
Geekbench's data for Galaxy S4 scores by Android version
The results of the testing were pretty conclusive, too; Geekbench scores for both the Note 3 and Galaxy S4 running Android 4.4.2 are significantly lower than those obtained when the devices ran Android 4.3. Geekbench assisted Ars' investigation by examining not just the scores of individual devices, but rather the full dataset of GS4s and Note 3s Geekbench has accumulated, making the results fairly difficult to dispute.
The conclusion, then, is pretty obvious: Samsung removed the offending code which caused the S4 and Note 3 to behave differently in benchmarking apps. Somehow I doubt they'll be trying that again anytime soon.