I spend a part of this evening fighting with ScriptManager.RegisterClientScriptInclude and had no chance to use it in a way that my javascripts would appear after MicrosoftAjax.js and in an order that I defined.
I finally found a solution, using ScriptManagerProxy and declaratively listing the javascripts in the order I wanted.
I was experiencing for some time a quite strange effect on my no so old installation of Windows Vista. After some dyas of usage without any reboot I sometime was unable to open any new window, it could be an explorer, internet explorer 7 tab, a menu of tray icon, and this without any error message. I first thought it was an issue with the video driver, but after too much annoyance I searched the web and found a post "Max Num. of Open Windows under XP/2003/VISTA - Resolved !' explaining the issue and a possible fix.
From Ohad's WebLog
Start++ is an enhancement for the Start Menu in Windows Vista. It also extends the Run box and the command-line with customizable commands. For example, typing "w Windows Vista" will take you to the Windows Vista page on Wikipedia!
See the full description on this page.