I doubt whether the CPU is running faster, the OS is clearly using the CPU much more efficiently now. The days of having a turbo mode on your computer are long over (a button that makes your computer run slower, yes they used to be common). It may be that there is some clocking change that was enabled now that they have improved stability, but I doubt that. The main issues of instability seem to be power related such as when you power your USB drive from the WiiU rather than externally so boosting clock speed and power consumption does not seem likely.
The chip likely has quite a bit of untapped potential, the powerpc architecture is a very decent one and this seems to have more in common with power7 than power6. RISC based processors are better for number crunching than CISC intel based ones. The WiiU has an OS in its infancy, I expect the performance to improve significantly over time especially when they better leverage the GPGPU features.
This is not unusual, I recently updated my laptop from a linux 3.5 kernel to a 3.8 one and saw noticeable speed improvements.
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