Custom PermaLinks - Weird Issue

We had an issue yesterday with our homepage not loading (white screen on browser, looks like it was waiting for response from site). The other pages on the same website loading normally. We tried it on different browsers (IE, chrome, FF) the issue was inconsistent i.e. the home page will load occasionally (a bit slow but entire content rendering fine) and would fail on refresh. Below are the things we did before the issue got resolved after some random attempts:
1 - Checked server CPU, memory & n/w utilization. All statistics within normal threshold range.
2. - Through wp-admin, clicked on “Update” button to force a save on the page. Flushed cache
of ‘W3 Total Cache’ plugin. Tested pages, it did not work.
3. - Noticed that the plugin ‘Custom Permalinks’ has a new update available. Upgraded plugin,
flushed cache and the issue got resolved.

We would like to understand what caused the issue so that in future we will be able to address it immediately if it repeats. Has anyone experienced this as well?

Details about our environment:
- Wordpress 3.2.1
- Stack: Ubanto 10.04.2 LTS, Apache2.2.17, MySQL 5.1.56, PHP 5.3.6
- Suspect Plugins (not all listed):
- Custom Permalinks
- Revision Control
- Server Name Support
- unFocus.Insensitivity
- W3 Total Cache
- WPsyslog

Appreciate any help, comments, support from the team.