Symptoms
Every third logon to Web Interface for SharePoint returns the following message:
"Web Part timed out"
If you refresh Internet Explorer, the icons load up.
Cause
The issue being seen is a feature of SharePoint and it is common to many portals. When the Web Part goes to get the data to display your applications, the Web Part uses an asynchronous mechanism built into SharePoint. If this takes "too long" it could prevent the rest of the page from rendering.
Resolution
To stop this poor behavior, the asynchronous mechanism has a time-out, which is 7 seconds by default.
You can change this setting by modifying the following element in the web.config of your SharePoint instance (the value is in milliseconds).
<WebPartWorkItem Timeout="7000" />
This is usually found at:
C:\Inetpub\wwwroot\web.config
You should "tune" this value based on your infrastructure.
More Information
For additional information, refer to CTX108349 – Web Interface for Microsoft SharePoint Administrator's Guide.