Resolution:
This is a known issue. Especially with big projects with lot of subfolders this happens.
The issue is fixed in the next release.For release schedules contact support@tibco.com.

Workaround1: After opening the project in File Sharing mode, Right click on Top root folder and Select "Expand All"
                             and then acquire resource.

Workaround 2: Bring Up designer and choose Administration tab -&gtConfigure Preferences, Check the Load Full
                              Project  and then load the project .Now with out doing Expand all, you will be able to aquire all
                              resources from the project root folder.

When Iopen a project in FileSharing mode and try to aquire resource from the Project root folder, It does not acquire some of the resources.