I'm not sure I have a clear enough picture. Hopefully I can help more if you can:
A. Post some example code - please make sure that the actual config settings you use are set as default values.
B. Describe the intent of your measurement. For example - you introduced some info about a trigger signal for a third counter, but I don't know how you intend that to relate to the first two counters where you see the problem.
C. Describe the nature of the error/problem. How is counter0 wrong when the signal is connected to both? Does the same kind of problem occur when operating counter1 alone? What exactly happens when trying to operate both at once?
D. Describe the physical wiring of signals into the connector block.
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