[Koha] Zebra problems

[All Saints Cathedral Library]

Hello All,
  
Recently we replaced our Koha 3.06 with a new install of Koha 3.16 on Linux Mint 13  XFCE via Ubuntu packages.  Since the upgrade, searching for books, both from the old database and recently entered, in both the staff client and the opac yields only books in the reservoir in the staff section.  

In the terminal it looks like Zebra is working, with errors for some, but not all, records:

exporting biblio 
==================== 
1..............................................................................101...............

3301..............................error retrieving biblio 3518 at /usr/share/koha/bin/migration_tools/rebuild_zebra.pl line 679. 
in/migration_tools/rebuild_zebra.pl line 679. 
.....error retrieving biblio 7462 at /usr/share/koha/bin/migration_tools/rebuild_zebra.pl line 679. 
7201................... 
Records exported: 7066 
==================== 
REINDEXING zebra 
==================== 
11:40:57-28/10 zebraidx(3813) [warn] Record didn't contain match fields in (bib1,Local-number) 
==================== 
CLEANING 
Zebra configuration information 
================================ 
Zebra biblio directory      = /var/lib/koha/cathlib/biblios 
Zebra authorities directory = /var/lib/koha/cathlib/authorities 
Koha directory              = /usr/share/koha/intranet/cgi-bin 
Lockfile                    = /var/lock/koha/cathlib/rebuild/rebuild..LCK 
BIBLIONUMBER in :     090$c 
BIBLIOITEMNUMBER in : 090$d 
================================ 
==================== 
exporting authority 
==================== 

Records exported: 0 
==================== 
REINDEXING zebra 
==================== 
skipping biblios 
==================== 
CLEANING 

I have tried resetting the permissions as described in the Koha wiki, but that did not help. Are there other permissions I should check?  Which ones?  What should the permissions be?  Should the user names and passwords for Mysql and Zebra and Koha all be the same?

When I investigated the path all the files seemed to be there, but the /usr/ bin/ zebraidx file is, according to gedit, “corrupted”.  Is that the problem?  What should be in it?  Can I remove it and download a single replacement file? What would the commands be?

I have also noticed that ' libmarc-xml-perl_1.0.1-1_all.deb ' is sitting in my home directory.  Where does it belong?  If I download it again as in the Koha wiki Koha on Ubuntu packages – long, I get a message “Permission denied”.
All the best,
Helen Belal
Volunteer librarian
All Saints' Cathedral Library