The problem is we have customers that have source control create copies of metadata that sends Architect into a fit creating duplicate components. So to counteract this I created a check when you load a meta file to be sure the userClassName inside the meta matches the file name it was read in from. The issue you guys are having is because the case is incorrect.
The Work around:
Rename the files w/ the proper case on disk prior to opening your project.
I'm going to have to change the file casing on write when users alter their userClassName by just case or simply be case insensitive with the meta validation. A bit more investigation is necessary.
Sencha Architect Development Team