on the admin caps, can you try adding them one at a time? on some machines, the js can be bit slow and the ‘click’ may not get taken if too close to the other one even though the color gets changed… not likely the issue, but would like to rule things out and doing just one cap update does…

for an example moderator, can you look in the db, in the wp usermeta table, for this users ID, can you look at their meta entry for wp_capabilities (your prefix might be other than wp_)…  would like to know the value before and after you try to add a cap…