I'm not sure why it didn't work either. I looked into the flashable zips and they seem just fine. It could just be me, or my phone. The CWM Recovery for the Atrix is terribly bugged and has been since day one of "Official Support" for the phone. So at times the recovery can by flakey, this is the first time I've had trouble flashing with it though. Oh well, I got the fonts on there anyway
Right after I posted, I pushed the files with ADB after renaming the ones on my phone so that I could revert back if I wanted to. That work perfectly for me.
For those wondering, here are the commands I used with a short explination of what they do.
1. adb remount
2. adb shell
3. cd /system/fonts
4. mv Clockopia.ttf Clockopia.bak
5. mv DroidSans.ttf DroidSans.bak
6. mv DroidSans-Bold.ttf DroidSans-Bold.bak
8. adb push Clockopia.ttf /system/fonts/Clockopia.ttf
9. adb push DroidSans.ttf /system/fonts/DroidSans.ttf
10. adb push DroidSans-Bold.ttf /system/fonts/DroidSans-Bold.ttf
11. adb reboot
Numbers 1 - 3 just set so that you can start to backup the fonts.
Numbers 4-6 move the stock fonts to new files names.
Number 7 gets you out of the ADB shell.
Numbers 8-10 push the new fonts onto the phone
Number 11 reboots the phone so that the changes take effect.
Note that you will need to have the three new font files in the folder you are working out of the command prompt in.
P.S. Looks awesome!!