I don't know if this is the answer but I remember seeing an article a while back about how the .air files for FS2002 were quite different from those for FS2004 - you can see for yourself if you use AI aircraft from the big sites like AI Aardvark, they include different flight dynamics for the different versions of FS.
If you watch addon AI traffic at a big airport you'll see some planes bob about on approach and after take-off because their flight model is not very stable so they are always seeking the right altitude which makes them go up and down a lot...
So my point is that EHM AI traffic was originally written for FS2002 and I think the planes' .air files might be FS2002 ones. If so, these might have trouble holding a stable altitude in FS2004 which causes them to rise and sink and therefore ATC keeps picking up their movement and asking them to correct it.
Of course I could be well out here (there are certainly bugs in the FS2004 ATC!) but it might explain what you are describing...