Assuming you are using good quality resins that have been handled/shipped/stored appropriately...
You should be getting a longer life out of the separate beds as you're using about double the amount of anion or cation resin compared to what is in a mixed bed cartridge. You have to look at the volume of each resin you're using, and the capacity of each.
In your case you may be comparing apples to oranges depending upon the resin that was actually sold to you. The mixed bed, cation, and anion may be from different manufacturers and have different capacities.