Datasheet
Rev. 3.00, 03/04, page 335 of 830
12.9.6 Mode Setting with Cascaded Connection
If the 16-bit count mode and compare-match count mode are set simultaneously, the input clock
pulses for TCNT_0 and TCNT_1 are not generated, and thus the counters will stop operating.
Simultaneous setting of these two modes should therefore be avoided.