I was flying along the coast to and from Texel two weeks ago and Amsterdam info had problems with my mode-S reception. I can only think of a bit of mud on the antenna after takeoff at Texel since the equipement passed the annual transponder check two days before and worked well for everybody except Amsterdam.
There must be a way to filter out all transponder replies with VFR codes or below certain altitudes. London and Paris have a lot more IFR/VFR traffic mix than Amsterdam and don't complain.
A few years ago, with another airplane, Amsterdam complained that we were inside the TMA, two altimeters and our alticoder showed that we were well below and we were asked to switch off the transponder. No complaints from anybody else. Aicraft are used weekly for IFR flights all over Europe.