Loud overtones after changing the nut?

The original nut of my Geddy Lee worn out, so I put a bone nut. Now several *fretted* notes (especially on the D & G strings) have loud overtones.

Fretted notes should not be influeced by the nut. So I don't understand why I'm hearing overtones that I didn't hear before. I didn't change the strings. Any ideas??

 

I already tested it. Nothing behind the nut is causing the overtones.

I just tested the bass for about 10 more minutes. During the first 5 minutes or so I didn't hear the offending overtones. But they came back!! Am I going insane or what? How is this possible?

 

I'm playing with a GK MB200 through a GK NEO112 cab. I'll change the strings and see what happens.

 

It was the strings! They were 2 year old Hi-Beams that I recently resurrected using denatured alcohol. It was my first try using denatured alcohol. I wasn't too impressed with the result. I'd rather buy new sets.

Anyway, it was my first try to replace the entire nut. I had to cut bottom corners of the premade nut because of the Geddy's neck binding. Interestingly, the Geddy required a flat-bottomed nut (not curved), so I sanded down the new nut. I ended up sanding too much and used an aluminium foil as a shim. It was a hack job. But now my Geddy sounds good and intonation all over the fingerboard is dead on.