Can you return them? If they're only two weeks old, you're always going to be better off with a single card solution.
On topic though:
I've seen periodic stutter like that when I was running distributed computing in the background. Even though it was running at a lower processor priority, it was killing my framerate every few seconds. Are you running boinc or folding@home (or *coin mining of any kind)? Even if it's not using the graphics card, boinc can cause microstutter.
Is this microstutter? You say the frame rate drops. Does it stay down?
Does GPU-Z report that crossfire is enabled?
Can you take one card out, cut your quality down a bit, and see if it plays smoothly with one card? If you don't want to wipe your install and start fresh, do you happen to have a spare HDD to get set up on just to rule out this as a software problem?
What software have you used to confirm your cards are being loaded? You said you monitored the frequency. During periods of framerate drop, was either your processor or graphics cards being maxed out? Were your frequencies dropping?
Can you verify that the card isn't running at low power clocks while you are in game? Using video acceleration in Flash can limit your card to 2d clocks. Meaning, if you have youtube in the background or minimized it will run terribly.
What resolutions and detail levels are you trying to game at? You said you changed the resolution to 1080, but what was it at before? Are you trying to push multiple monitors with these cards? I have a single 7770 in a linux box, and it's great in terms of power per watt, but really it's a lower midrange card.
A lot more information and specifics would really help.