Is there a way to change the layout of Windows Start window?
Whenever you open an application, (or a menu, or a document) Windows has to load that object into memory. If you don't have enough available (unused) memory, it swaps whatever has been sitting in memory the longest without being used to your hard disk, freeing up some memory. That disk space is usually called the swap file. Since hard drives are mechanical, they are much slower than computer memory.
So, the more memory that your computer has, the more things you can open/start/launch/do before Windows has to start swapping out to that sloooooow hard drive. Your All Programs menu problem is a symptom of doing more stuff than your computer has memory to handle. Note that you could still see those symptoms with 4, 6 or even 8 Gig of RAM, depending on how much stuff you do.
Solution 1: add more memory
Solution 2: this won't fix your memory issue, but it will stop one menu (like the All Programs menu) from getting in the way of other menus. The problem is that Windows has a "delay" of .4 seconds from the time the mouse pointer hovers over a menu to the time it starts to expand that menu. By making that delay really long, menus only open when you click on them.
To fix this, you must edit the Windows Registry. You can literally break Windows if you delete or change the wrong setting in the Registry, so proceed with caution. Click Start, (in XP click Run next), type regedit, press Enter, navigate to HKEY_CURRENT_USER \Control Panel\Desktop. Look for an entry called MenuShowDelay. If it's not there, right-click an empty spot in the window and select New\String Value. Type MenuShowDelay and press Enter. Now double-click MenuShowDelay, and give it a value of 65000. The start menu, taskbar, and menus will now stop auto-appearing, and must be clicked on to open.