you mean to say that baud also changed?
The register : Clk_ctrl can be checked. see the xmega manual.
when writing this register, it is protected so i can not image that it would change.
Maybe you can check the errata.
When the speed changes, try to measure if it is really exact. and check the errata of the chip.
maybe you use external xtal or clock and the oscillator fails?
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