Pickups with strong magnets directly under the strings act on them like a small brake. Players sometimes call the warbling effect "Stratitis," because it's common on guitars with three single coils.
Symptoms:
- Low E and A notes above the 12th fret sound out of tune or wobbly
- A strange beating or chorus sound on sustained notes
- Intonation that won't set correctly no matter how you move the saddle
- Sustain that dies early
How to fix it:
- Lower the neck pickup's bass side first. It sits where the low strings swing the widest.
- Lower the other pickups slightly on the bass side as well.
- Play the low strings at the 15th to 17th frets after each small adjustment.
- Stop when the warble is gone, then raise slightly if you lost too much output.
- Recheck intonation once the pickups are set.
If you recently switched to a heavier set, the bigger strings swing closer to the pickups, so the problem can appear after a gauge change even if nothing else moved.