Hi, mariomoskis,
Unfortunately this is part of the limitation of Scan Mode. You can basically think of scan mode like a train that goes around to all of the modules collects data and drops it off at the controller, and there is only 1 train for the entire device and it only runs at one speed (scan rate). The train makes a pass every scan rate interval, so if you want to output a pulse train at slightly less than 1 kHz you will get aliasing. However, cRIO should not disconnect at all, I don't know what's the matter there, but it seems to be closely related.
There are two solutions to this issue, but both would require some changes.
1. You can avoid all of these issues and get down to a 25ns (or smaller) time resolution if you move into FPGA mode. We can use existing code from NI.com/IPnet to implement a pulse train generator with custom timing settings and pulse times on any module.
2. Certain modules support specialty digital modes, that basically deploy a pre-built section of FPGA code (in scan mode) that support certain common functions like Pulse Width Modulation. With these modules you can request specific a rate (which will update at 1KHz) , but the actual timing for the module is handled in the hardware. There are only a few modules that support this and they are listed in the link below.
KB 55L06EMO: What C-Series Modules Support Specialty Digital Functions in Scan Mode?
http://digital.ni.com/public.nsf/allkb/2664A3D35D9F79A4862576B300277E35?OpenDocument
I hope this helps.
Saludos!
Jesús
