A while back we opened a support ticket regarding the use of the AxUpdatePortal utility (which is the only way to update EP in a 64-bit environment after SP1). This post summarizes the role of the axwebparts.cab, how misuse of the AxUpdatePortal utility can "break" EP and the way to resolve the issue when it does occur.
In extreme circumstances, it is required to re-run setup for EP, which is slow, but once you are familiar with the steps, you can reliably use AxUpdatePortal.
http://blogs.msdn.com/emeadaxsupport/archive/2009/07/23/axupdateportal-exe-does-not-update-enterprise-portal-when-not-running-from-an-elevated-command-prompt.aspx
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