2.9.2 - Timer Operation/Performance Notes [U3 Datasheet]
Note that the specified timer clock frequency is the same for all timers. That is, TimerClockBase and TimerClockDivisor are singular values that apply to all timers. Modes 0, 1, 2, 3, 4, 7, 12, and 13, all are affected by the clock frequency, and thus the simultaneous use of these modes has limited flexibility. This is often not an issue for modes 2 and 3 since they use 32-bit registers.
The output timer modes (0, 1, and 7) are handled totally by hardware. Once started, no processing resources are used and other U3 operations do not affect the output.
The edge-detecting timer input modes do require U3 processing resources, as an interrupt is required to handle each edge. Timer modes 2, 3, 5, 6, 9, 12, and 13 must process every applicable edge (rising or falling). Timer modes 4 and 8 must process every edge (rising and falling). To avoid missing counts, keep the total number of processed edges (all timers) less than 30,000 per second (hardware V1.21). That means that in the case of a single timer, there should be no more than 1 edge per 33 μs. For multiple timers, all can process an edge simultaneously, but if for instance both timers get an edge at the same time, 66 μs should be allowed before any further edges are applied. If streaming is occurring at the same time, the maximum edge rate will be less (7,000 per second), and since each edge requires processing time the sustainable stream rates can also be reduced.