In build 971 Architect started checking the signature of meta files it read in. Mainly this was due to outside applications creating copies (tmp) of meta and Architect getting confused. The meta file name now must match the userClassName stored inside of it. This tells Architect it's a legit meta file and not something created by source control or another IDE.
Some of you might see a screen like this one when you open up your project:
Screen Shot 2013-05-24 at 10.30.35 AM.png
Architect will not remove these files but each time you open up the project you will get this screen.
Fix: the fix is to change the filename to match the userClassName found inside the file, in this case MyCheckboxGroup2
The filename should be changed to MyCheckboxGroup
I'm unsure how "valid" files could get out of sync like some users have reported. My guess is older versions of Architect...
Also note that if you already have a file by that same name be sure not to overwrite what's possibly the newer valid version of your class.