Took some time today to wire up an inverter between STOP and START. The results are - interesting.
Instead of steady 1µs measurement I get two clusters, one at 1µs and one at 3µs. Both in itself are stable, but the measurements jump randomly between the two.
Not SPI weirdness, I took a scope to the SPI bus and decoded the line protocol, the values I read in the software are actual, visible on the line.
There difference between the clusters is only from the TIME1 register, it jumps to and fro between them.
However, In "mode 2", TIME1 is the ring oscillator count from start to the next rising edge of the clock input. The clock input is 10MHz, so I cannot quite see how even a missed edge there could amount to a 2µs offset. There must be something very odd in my calculation. Something wrong with the LSB calculation from the calibration values, I guess.