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Choosing Windows boots Linux

This can have many different reasons. Check these first:

If you have both Windows and Linux installed on the same internal disk, and choosing Windows in the rEFIt boot menu boots Linux, the likely cause is that your Linux system installed its boot loader (GRUB, LILO, etc.) in the Master Boot Record (MBR) instead of the partition boot record (PBR). Due to the way rEFIt works, choosing either of the operating systems in the rEFIt menu starts the Linux boot loader installed in the MBR. In the best case that boot loader then presents you with another menu where you can choose between Windows and Linux, and in the worst case it just loads Linux without giving you a chance to get into Windows.

You can confirm that this affects your system by running the “Partition Inspector” application that is on the rEFIt disk image, and is usually installed under /Applications/Utilities. When you run it, it looks at the partitions and file systems on the first hard disk, and generates a report. You are affected if the report contains something like this:

MBR contents:
 Boot Code: GRUB

To fix this problem, you need to install GRUB / LILO in the boot sector of your Linux partition instead, then remove it from the MBR. I’m not aware of a ready-made tool that can safely do that removal. Please ask for help on a Linux forum if needed.