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Hardware related question

First I apologize for asking a seemingly non-Keil related question.
I have 2 evaluation boards (STM32 Olimex and another, home-made). Their grounds are connected, supply is separate. Both are connected to a TCP/IP network. I am sending a signal (about 56 KHz) from one to the other via a wire, and the decoding of that works, but not always: automated tests that verify the software fail (while manual tests work...) after programming an board chip on one of the boards plus an FPGA. When I say fail I mean that the target board does not send out a reply via the network indicating it decoded the 56 KHz successfully.
I have noticed that I can rectify the situation by either connecting a probe to the signal pin at the receiver and the ground it to the common ground, or connect a ST-Link V2 to the Olimex board. This begs for to be grounding/parasite capacitance problem, but how can I determine that let along solve it?
Thanks in advance

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