A little update, if I press play on Reaper everything keeps working again. If I disconnect and re-connect the main plugin everything go to hell again.
There must be something concerning the communication between Reaper and VEP.
EDIT
Further testing shows me that if I go to start audio engine everything goes to work again, till the next connection where it loose everything again. So I need to click on the audio engine button everytime.
Another thing I noticed is that when I put the play cursor perfectly aligned with a note (quantized with the grid) the note doesn't play, I always have to put the play cursor before the note to hear a sound.
It doesn't happen with an instance of Kontakt loaded directly in Reaper....