Hi,
How you connect your AI signals depends on how you configure your PCI-1200, but for this application I reccomend using a Differential Input configuration. The AI Channels 0 & 1 can be used as a differential pair and should produce desired results providing you conform to the differential grounding reccomendations on page 3-8 (29/93) of the manual (http://www.ni.com/pdf/manuals/320942d.pdf). If implimented correctly, this method should largely illiminate the 50Hz noise that you are currently seeing.
If you have already tried this to no avail please give more details of the hardware connections used (in words please since the ASCII images seem to be displaying incorrectly on my browser) and also details of the software that you are using to acquire the information, for example if you are using a LabVIEW Virtual Instrument please attach the .vi file along with an explanation and I will do my best to help you out.
Best Regards,
Ian Colman
Applications Engineer
National Instruments UK & Ireland