I have been hit by issues with the Solr 4 system shipping with Alfresco 5.0.b. For me it surfaced as ACE-3037 (‘Category Root’ is empty on the Admin tools page), but there seem to be further problems (ALF-21127 and ACE-2950). For those brave enough, there is a replacement jar file available for download below. To apply the fix, stop the system, replace solr4/WEB-INF/lib/alfresco-solr4-5.0.b.jar with that file, rm -rf alf_data/solr4/*/* and start up again. That solved the problems for me. A patch against 5.0.b sources is at Github. Good Luck! ;)
Download Solr4 Fixes for Alfresco 5.0.b
