Hello Nacho,
the output terminal of the AI Start VI will never be able to give you the actual rate when you use external clocking. It's only valid whenever you use internal clock (and the board divides down the master clock to get as close as possible to the desired rate). This is what you get at the output.
You can test this by using an example with internal clock and choose a "rare" frequency/rate such as 1621.5. The board will really sample at a similar rate, but not always at the exact speed you may choose.
If you want to calculate the frequency, you'll have to use counters and feed the encoder signal (CH A) to the counter's source (or gate depending on which method you use to compute the frequency).
Regards,
Jorge M.