Firefox 4 has added some eye candy that greys out the webpage when an alert appears. This looks nice but is very slow over a remote desktop connection as it forces the entire window to be sent again to the client.
To fix, just add this to the end of userChrome.css
tabmodalprompt {
background: transparent !important }
The file should be found here: C:\Users\$username\AppData\Roaming\Mozilla\Firefox\Profiles\$letters.default\chrome\userChrome.css
If it doesn't exist then copy and rename userChrome-example.css to userChrome.css
Firefox 4 Remote Desktop