This is a strange error - can I ask for some background on your installation? E.g. do you have a default installed Alfresco bundle or did you deploy the WAR yourself? Also did you make any changes to the setup? I'm asking because both the problems you are having suggest the server cannot find the index files or that they are out-of-date as the location for the file/indexes are relative to the start directory for your installation. If you changed the start dir then this would cause this problem i think.
Thanks,
Kevin