If bleeding doesnt help, check your caliper pistons. As silviefox suggested, could be scoring or corrosion on the pistons.
When you change pads, you push the pistons back. Since new pads are thicker, less piston sticks out past the seals. If you had corrosion on the portionnof the pistons that were sticking out past the seals with the old (thinner) pads, now that corrosion could be running across the seals and hanging up. You may be feeling it binding, then releasing as it pushes out past the seals.
Im probably doing a bad job explaining this, but if all else fails its worth taking a look at the pistons to see if they are nice and smooth or scored up. If they have slight corrosion you can often clean them up. If they look good, see if the seals are seated well also. You can get corrosion in the groove that the seals sit in which will push the seal out causing the piston to bind up. That usually results in a dragging brake symptom though.
Ive done nothing to the brakes on my Versys thus far, so i technically have zero experience working on these brakes, but Ive had these issues on another bikes with twin piston Tokico calipers like the ones on the V