Hello Balaji,
Thank you for contacting National Instruments.
There should be no reason for one counter on your machine to affect the other counter. If the counters work correctly initially, there is nothing on the board that will cause them to create this effect after a long period of running. Basically, the counters will either work correctly or not at all.
What usually causes problem such as these is noise in the external environment. What I would try to look for is a change in your external environment when this problem occurs, such as a piece of machinery turning on or some other noise source.
Please let me know if you determine any additional information on this issue.
Regards,
Bill B.
Applications Engineer
National Instruments