When you select a (software) instrument track, it does not immediately switch into live or performance mode. You must send a MIDI event before live mode is activated, which takes around 100 ms to engage, and this is more than enough to destroy the timing of your first played note.
If you require perfect timing for the first played note, you need to send silent MIDI events in advance—you can press the sustain pedal and make a small move of the pitch bender or modulation wheel, for example. This will turn on live mode. For details, see Understanding Live Mode.