Simplest solutions win:
If you have spare filter in your synth, set it in series after the first one, set it to highpass and turn key-tracking all the way up. Here you go. Fundamental-killer.
Also, I find this bad habit being a result of dialing LP cuttoff down while having EQ (with high pass) on. It distorts your perspactive. So you can try this: Turn off your eq, slowly rise LP cuttoff until it sounds better (but not too much, just slowly) and then re-aply EQ. That also helps.
...you can get pitch tracking EQs, but they tend to be really experimental and I wouldn't trust them too much on vital sounds. Fixing it some simpler way is imho better.