added a comment - - edited
I don't think this should be a Minor priority because it stops backups completing.
I'm encountering this problem also.
The Cron job on one site is failing (the Cron job does start, and other sites on same server are completing without problem).
I've checked the database using MySQLAdmin - no problems.
Updated site to the latest version: Moodle 1.9 + (Build: 20080409) (vanilla installation aside from Themes).
But the Cron is still just stopping at 'Checking glossary module for additions.' (see below)
After suggestion from Eloy I checked all courses for instances of the Global Search Block.
Moodle reported 7.
So I went to each course and deleted them - but there were only 4.
See screenshot attached that shows Moodle reporting 3 instances of the Global Search block (but this figure is not linked to any courses!)
So, I disabled the Global Search block, and then removed var/www/.../blocks/search and it works OK 
Original error message follows
(thanks Stuart):
Starting activity modules
Processing module function assignment_cron ...done.
Processing module function chat_cron ...done.
Processing module function forum_cron ...Starting digest processing...
Cleaned old digest records
done.
Processing module function scorm_cron ...done.
Processing module function workshop_cron ...done.
Finished activity modules
Starting blocks
Processing cron function for rss_client....
http://computerworld.co.nz/rss/computerworld.xml ok
[Martin D deleted some links here]....
http://www.checkpoint-elearning.com/rss/index.xml ok
58 feeds refreshed (took 1.58687 seconds)
done.
Processing cron function for search....
-DELETE---
Starting clean-up of removed records...
Index size before: 1052
Checking chat module for deletions.
No types to delete.
Finished chat.
Checking data module for deletions.
Finished data.
Checking forum module for deletions.
Finished forum.
Checking glossary module for deletions.
Finished glossary.
Checking lesson module for deletions.
Finished lesson.
Checking resource module for deletions.
Finished resource.
Checking wiki module for deletions.
Finished wiki.
Finished 0 removals.
Index size after: 1306
-UPDATE---
Starting index update (updates)...
Checking chat module for updates.
No types to update.
Finished chat.
Checking data module for updates.
Finished data.
Checking forum module for updates.
Finished forum.
Checking glossary module for updates.
Finished glossary.
Checking lesson module for updates.
Finished lesson.
Checking resource module for updates.
Finished resource.
Checking wiki module for updates.
Finished wiki.
Finished 0 updates
-ADD------
Starting index update (additions)...
Index size before: 1052
Checking chat module for additions.
No types to add.
Finished chat.
Checking data module for additions.
Finished data.
Checking forum module for additions.
Finished forum.
Checking glossary module for additions.
Bug
Closed
Minor
I don't think this should be a Minor priority because it stops backups completing.
I'm encountering this problem also.
The Cron job on one site is failing (the Cron job does start, and other sites on same server are completing without problem).
I've checked the database using MySQLAdmin - no problems.
Updated site to the latest version: Moodle 1.9 + (Build: 20080409) (vanilla installation aside from Themes).
But the Cron is still just stopping at 'Checking glossary module for additions.' (see below)
After suggestion from Eloy I checked all courses for instances of the Global Search Block.
Moodle reported 7.
So I went to each course and deleted them - but there were only 4.
See screenshot attached that shows Moodle reporting 3 instances of the Global Search block (but this figure is not linked to any courses!)
So, I disabled the Global Search block, and then removed var/www/.../blocks/search and it works OK
Original error message follows
(thanks Stuart):
Starting activity modules
Processing module function assignment_cron ...done.
Processing module function chat_cron ...done.
Processing module function forum_cron ...Starting digest processing...
Cleaned old digest records
done.
Processing module function scorm_cron ...done.
Processing module function workshop_cron ...done.
Finished activity modules
Starting blocks
Processing cron function for rss_client....
http://computerworld.co.nz/rss/computerworld.xml ok
[Martin D deleted some links here]....
http://www.checkpoint-elearning.com/rss/index.xml ok
58 feeds refreshed (took 1.58687 seconds)
done.
Processing cron function for search....
-
DELETE---Starting clean-up of removed records...
Index size before: 1052
Checking chat module for deletions.
No types to delete.
Finished chat.
Checking data module for deletions.
Finished data.
Checking forum module for deletions.
Finished forum.
Checking glossary module for deletions.
Finished glossary.
Checking lesson module for deletions.
Finished lesson.
Checking resource module for deletions.
Finished resource.
Checking wiki module for deletions.
Finished wiki.
Finished 0 removals.
Index size after: 1306
-
UPDATE---Starting index update (updates)...
Checking chat module for updates.
No types to update.
Finished chat.
Checking data module for updates.
Finished data.
Checking forum module for updates.
Finished forum.
Checking glossary module for updates.
Finished glossary.
Checking lesson module for updates.
Finished lesson.
Checking resource module for updates.
Finished resource.
Checking wiki module for updates.
Finished wiki.
Finished 0 updates
-
ADD------Starting index update (additions)...
Index size before: 1052
Checking chat module for additions.
No types to add.
Finished chat.
Checking data module for additions.
Finished data.
Checking forum module for additions.
Finished forum.
Checking glossary module for additions.
DELETE--- Starting clean-up of removed records... Index size before: 1052 Checking chat module for deletions. No types to delete. Finished chat. Checking data module for deletions. Finished data. Checking forum module for deletions. Finished forum. Checking glossary module for deletions. Finished glossary. Checking lesson module for deletions. Finished lesson. Checking resource module for deletions. Finished resource. Checking wiki module for deletions. Finished wiki. Finished 0 removals. Index size after: 1306 -UPDATE--- Starting index update (updates)... Checking chat module for updates. No types to update. Finished chat. Checking data module for updates. Finished data. Checking forum module for updates. Finished forum. Checking glossary module for updates. Finished glossary. Checking lesson module for updates. Finished lesson. Checking resource module for updates. Finished resource. Checking wiki module for updates. Finished wiki. Finished 0 updates -ADD------ Starting index update (additions)... Index size before: 1052 Checking chat module for additions. No types to add. Finished chat. Checking data module for additions. Finished data. Checking forum module for additions. Finished forum. Checking glossary module for additions.