Microsoft SharePoint designer 2007 is a tool supposes to be helpful when it comes to changing design of master pages and SharePoint web pages.  But yet there is always some bugs in the tools.

If you open a SharePoint master page using SharePoint Designer (lets say the \12\Templates\Layouts\application.master), it will automatically change the paths of the loaded controls, and if you save, the SharePoint pages will no more work ! A global error will appear:

"The file '/_layouts/_controltemplates/TopNavBar.ascx' does not exist)"

Even if you try to undo the changes, but yet the SharePoint designer saves the correct version of the control paths and ignore your changes. So to solve this problem, just change the path of the referenced controls. So instead of having _layouts/_controltemplates/whatever.ascx or _controltemplates/whatever.ascx, just set the path to

../_controltemplates/whatever.ascx

In this way, it will load the controls correctly and the pages will open again.

So this is the main bug in the SharePoint designer!  Although it is an amazing tool to set the controls and fix the design, but yet one has to be careful while using it!