EFI problem after installing Ubuntu 11.04 on Macbook 5,2

Hello,
I have a Macbook 5,2, on which I'm triple booting OS X - Linux - Windows, using bootcamp and rEFIt.

I had a variation of Ubuntu 10.04 called Uber Student as the linux installation.
I installed Ubuntu 11.04 AMD64 instead, by choosing the EFI boot option.

Now this gave me some problems. When I shot down, the Macbook gives me a troubling long beep sound.

When I start up, I'm still able to boot up into rEFIt and Grub2, but there is a big delay with the screen being black for about 30 seconds and the little white light in the left corner of the Macbook is blinking feverishly.
What is going on here? What's up with the scary beep sound and the long boot up delay?
Secondly, when I want to do an update of the Ubuntu system, the update manager asks me to do a partial upgrade, which includes removing the grub-EFI, resulting in a system that won't boot...
Any ideas what the problem can be?
Thanks, Kasper