Always check register.mcselec.com ! The enhancements/bugs contain info about changes since the release :
xmega, config OSC : when using external osc, enable the internal osc as well.
So for you : Config Osc = Enabled , Extosc = Enabled , Range = 12mhz_16mhz , Startup = Xtal_256clk , 32khzosc = Enabled
This is a bug caused by an improvement. the improvement is to wait for the status bits till the oscillator is ready. But when not using the internal osc, this bit can become 1 despite it is not enabled, leading to a wrong compare.
So as a workaround, enable the internal osc.
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