After upgrading from VMware ESX 3.x to ESX 4.0 you can cleanup the bootloader from the older ESX 3.5 installation. You can do this from the console of by connection the host with ssh, give the command “cleanup-esx3”
Little note: You can run the cleanup-esx command as long as everything works for you in 4. If you use the -f flag, the software prompts you to confirm that you want to disable the ability to roll back to the ESX 3.x.x.
Thanks xchello from Dutch VMug for the tip!