Hi Pilo,
Are you using a PXI-6035E or a PCI-6035E?
One source could be the cb-68LP, this connector block is not shielded and might be picking up some noise.
Could you try the accelerometer on a different channel, say 6 and 15. Then if that doesn't work try the accelerometer signal as a NRSE signal and connect to CH3 and GND.
Just a suggestion, but I need to know what form factor your DAQ card is, and the voltage of the frequency signal.
Regards
JamesC
Applications Engineer
NI UK