Lately I have seen the issue when we run AxUpdatePortal (AxUpdatePortal.exe -updatewebsites -verbose -iisreset) , the process is reading following registry keys:
SOFTWARE\Microsoft\Shared Tools\Web Server Extensions\14.0
SOFTWARE\Microsoft\Shared Tools\Web Server Extensions\12.0
Then AXUpdatePortal is doing IISReset and report Success. You are unable to see that web parts, proxies are deployed or page being upgraded. After successful running on AxUpdatePortal the page is simply not updated.
The reason behind is that user running AxUpdatePortal does not have correct rights for SharePoint, this is why nothing is happening.
To verify your rights please follow: http://blogs.msdn.com/b/axsupport/archive/2011/05/31/permissions-needed-to-run-axupdateportal-exe.aspx