This is a frustrating issue and I haven't seen it discussed anywhere else, so I'll add this to the ether.
If you are using Microsoft Dynamics CRM 4 and the Outlook plug-in for CRM4, you may find that the "Customization" option in CRM will dissapear for no apparent reason. BTW --It can also affect other CRM options.
The problem seems to be a conflict between CRM and the Outlook plug-in, so if you launch CRM first, you will see the option, if you launch Outlook first, you will not. However, having said that, eventually the option will probably dissapear even if you start both apps in the right order.
Update: one of my colleagues has told me that using the fully qualified name of the CRM server will also help with this issue. so instead of http://machinename you would use http://machinename.domain to open CRM. I haven't tested this yet.