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When a synchronized project is first created (using content on a remote system), the Project Auto-Sync Settings are set to Sync None so the project does not synchronize. This is confusing, because the user expects the project to appear in their workspace, not to have to manually synchronized before it appears. Instead, the Project Auto-Sync Settings should be set to Sync Active by default.
Actually, Sync Active is the default, and projects are normally synchronized on creation. However, I reproduced the behavior you described with the following steps: 1) Create a new synchronized project 2) Set it to Sync None 3) Delete the project 4) Recreate a new synchronized project with the same name. So maybe you were reusing an old project name. Admittedly, this is still a bug, but for a different reason.
I may very well have reused the same name. I just tried a completely new name and it seemed to synchronize ok.
Should be fixed as part of Bug 371507. Data is no longer stored by project name.