That error message "Repository 'nbeportal' is still not fully initialized after 10 minutes" has nothing to do with indexing. "Initialization" refers toModeShape attempting to start up and initialize a brand-new repository; e.g., define all the namespaces, register the built-in node types, load initial content (if any), etc. For a local cache, there is no way this should take 10 minutes; it should take just a fraction of a second.
I suspect that it has something to do with copying the Infinispan cache storage files. Those files should represent an already-initialized repository, which means that upon startup ModeShape shouldn't have to do any initialization. So perhaps those files were corrupt or incomplete?
I'd suggest turning on debug logging for ModeShape (e.g., "org.modeshape" logging context) and Infinispan (e.g., "org.infinispan").