NetBeans 6.9 contains a feature that automatically looks for external changes to keep informations about files up-to-date. We have some reports that it can slow down NetBeans mainly, when an open project has many folders. When NetBeans find out that files were externally changed, it re-scans the files to keep data up-to-date that are used with features like code completion, navigation etc. Unfortunately the notification and following re-scanning can take some time and during this time many mentioned features are waiting for the finishing of scanning. There is option Enable auto-scanning of sources that can switch off this behavior. The option you can find it in Options dialog, Miscellaneous category and Files tab.
The default behavior is that NetBeans also looks for external changes when the main window gets focus. This is can be during developing a web application very often when user switches between browser and IDE. The mentioned option also switch this off.
When you switch off option Enable auto-scanning of sources you can still keep the information up-to-date, just invoke Scan for External Changes action from Sources menu manually.