Wayuu,
according to what you say, it seems fairly clear that the board is not missing pulses and that those pulses are a clean signal.
What comes to my mind now is... Why do you say that you get more cycles? I mean, if you always get the number of samples you request, what's the problem? Maybe a delay between channels?
If that's the case, then it may have something to do with the interchannel delay parameter.
You can change the value of this parameter with the AI Config vi.
I would first check these links below that talk about it, and see if the behavior you are seeing is just an effect of your board having a unique ADC and hence a delay between samples of different channels.
http://digital.ni.com/public.nsf/websearch/9AE87416C8792FC286256
D190058C7D3?OpenDocument
http://zone.ni.com/devzone/devzone.nsf/webcategories/E8C00D6CC2BDD44386256882001425DA?opendocument&node=
Regards,