rEFIt just launches GRUB; there's no real "sync" between the two programs. Chances are you've got a BIOS-mode GRUB installation with a hybrid MBR to tell the Mac's firmware to activate its BIOS (aka CSM or legacy) support. This is a poor way to do things because it's dangerous and it can create problems like the one you've encountered. I recommend you instead try an EFI-mode boot of Linux using another boot loader. If you're using a 3.3.0 or later kernel, you can do this directly by upgrading to rEFInd (a fork of rEFIt that I maintain; rEFIt has been abandoned for close to four years now):
- Install rEFInd in OS X. (Alternatively, you can test this from rEFInd on a USB flash drive or CD-R, although some Macs have problems booting these images. These images include all the necessary filesystem drivers, so you needn't install them for such a test.)
- Install the EFI filesystem driver for whatever filesystem holds your kernel (normally ext4fs).
- When you reboot, select one of your Linux kernels, press Insert or F2 twice, and add
ro root=/dev/sda6. (It's probably
/dev/sda6, given the information you posted; but if it's something else, change that appropriately.) When you press Enter, Linux should boot.
- In Linux, run the
mkrlconf.sh script that comes with rEFInd. Be sure to run it as
root or by using
sudo. This step creates a file called
/boot/refind_linux.conf that holds kernel options, thus obviating the need to edit them, as in the previous step.
Thereafter, you should be able to boot Linux directly from rEFInd without using GRUB and without editing the boot options via F2/Insert. You may even want to replace your hybrid MBR with a standard protective MBR. (Don't do this if you're triple-booting with Windows, though.)
You can check out my page on EFI installations of Ubuntu on Macs for more on this topic; but that page is written for somebody doing a fresh installation. Thus, it covers much more than you need to do.