Joe van Tunen - 2010-08-11

rEFIt is not responsible for the boot process after it displays the penguin except for a couple things:
1) Display penguin
2) Set the active partition flag in the MBR and also set the MBR boot code if there isn't any.
3) Write to NVRAM the Boot Camp disk to boot. The legacy loader starts looking for bootable disks starting with the disk that is set in NVRAM. This is a new feature of rEFIt that is not done in the current 0.14 version.
4) Get the legacy loader info from Apple's EFI
5) Start the legacy loader

The legacy loader starts the BIOS which executes the boot code on the MBR of the first disk it finds that has an active partition (starting with the Boot Camp disk that is set in NVRAM).

Do you see anything different when you bypass rEFIt by holding down the option key at startup to use Apple's boot loader?