This is more likely normal timelapse flicker from the aperture than a failing shutter.

On many DSLR lenses, the aperture stays wide open between shots and the camera stops it down for each exposure. Tiny shot-to-shot differences in where the blades land can cause small brightness changes, which become obvious in a timelapse. That effect is often worst at intermediate apertures and much less noticeable at the aperture extremes, where the blades hit a physical stop.

Your test fits that pattern: at f/3.5 (wide open) and at f/22 (fully stopped down), variation is reduced because the aperture is at an extreme position. So the flicker you saw is not good evidence that 1/4000 s is inaccurate or that the camera is worn out.

If you were truly in manual exposure, metering mode should not change exposure, though auto settings or bracketing would. A physical shutter issue is possible, but based on the behavior described, aperture variation is the more likely cause.