So I was trying to remove an add-in from starting up with VS.NET but when I open the “Add-in Manager” dialog through Tools->Add-in Manager… menu, Startup check-box for that add-in is disabled so you cannot un-check it. You see something like this:
It turns out this is caused by the .addin files of respective add-ins being read-only. This happens on Vista and Windows 7 due to UAC since these files are in Program Files folder.
Fix is simple, run VS.NET as administrator so you can uncheck Startup box for add-ins in Add-in Manager. Right click the shortcut for VS.NET and choose “Run as administrator” and presto, all check-boxes are enabled now.