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QjackCtl just reports the exact sample-rate the jackd server is actually driving the sound-card device.

That means, if you asked for a 96Khz sample-rate for instance on the jackd command-line and it ended as 48KHz on the QjackCtl panel (which as said is the final value reported by jack itself) then it is quite probable that your audio device or driver does not support functioning at 96Khz and it just fallback to 48Khz. Business as usual ;)

Cheers