Hi GhastMaster,
The most likely problem would be your desktop is set to "Automatically align icons".
If you right click on the desktop and select "Arrange Icons By" and then "Auto Align", this might help.
unfortunately it's been a while since i've had icons on my desktop (since windows 98) so i'm not too sure if it'll work as it used to
Not sure as to why your custom start button changes - most likely because it's not done 100% - in which case we can't help you out in that regard.