Take all the saddles out again, and line them all up side by side on a flat surface. Look at them end on, and you should see the correct order they are meant to be placed on the bridge - they should follow the convex of the fingerboard i.e. low ones on the outside, slightly higher ones in the middle.
Also, when I last took my floyd apart, there was a metal shim which is meant to be placed under the four inner saddles. If yours had that, be sure to fit it back exactly where it was if it dropped out accidentally.
edit: Just read that you've replaced some of the saddles with other ones you've got elsewhere. In that case, a replacement set is probably your best option and should cure the problem.