"Input filter" option is not for signal quality, but for step pulse (or any other input mode) jitter & noise reduction. It also smoothens motion if input multiplication is being enabled on drive (like moving 5 counts on one step pulse).
I think it actually might be tuning issue. When you run test responses on GDtool, the motion profiles are flawless (no jitter etc at all). But from external sources there will be always even little bit of it which may make badly tuned system to react badly.
To test this, try adjusting acceleration to maximum from GDtool trajectory planner and do some step response tests (low, medium and large amplitudes). The sharp acceleration profile may reveal something that smooth curves didn't.