Yes they are the "wrong" way round, but that's MS for you.
boot = windows
system = boot files
active = start here
It causes no end of problems. People say "I've put everything on the boot disk, and it still doesn't work" because they see that "boot" flag.
But we tend to use the term in its english language sense, and those flags have a specific non-intuitive meaning to the MBR
Here's the Vista Help item on the subject
What are system partitions and boot partitions?
System partitions and boot partitions are names for
partitions or
volumes on a hard disk that Windows uses when starting. These technical terms are only important if you have more than one operating system installed on your computer (often called a dual-boot or multiboot configuration).
The system partition contains the hardware-related files that tell a computer where to look to start Windows. A boot partition is a partition that contains the Windows operating system files, which are located in the Windows file folder. Usually, these are the same partition, especially if you have only one operating system installed on your computer. If you have a multiboot computer, you will have more than one boot partition. An additional term, the active partition, describes which system partition (and thus which operating system) your computer uses to start.
When you turn on your computer, it uses information stored on the system partition to start up. There is only one system partition on a Windows-based computer, even if you have different versions of Windows installed on the same computer. However, non-Windows operating systems use different system files. In a multiboot computer using a non-Windows operating system, its system files are located on its own partition, separate from the Windows system partition.
A boot partition is a partition that contains Windows operating system files. If you have a multiboot computer that contains, for example, this version of Windows and Windows XP, then each of those volumes are considered boot partitions.