Windows 2000 likes only one partition with the *ACTIVE flag on a system. I DON'T MEAN THE "/boot" LABEL!!!!! If you are using grub or lilo, the Linux hard-drive should not be set as boot--it is still technically booting from your primary (windows) drive's "Master Boot Record". (Make a boot-floppy before changing anything.)
If you don't know what I mean by the *boot flag on the first partition of each hard drive--don't change anything until you do.
Just for interest, there is an entry you can put into the win.ini file to tell it not to check the second drive, nor any of the partitions within it. By default, the program checks for all drives, all partitions, and looks at the file systems. But, that doesn't take long with only two drives. As the other person said, the boot-loader can make a difference also. I use lilo, but in the past have used grub with good results.
You might also check the boot.ini file on W2k as well, it may have written a partial entry for the second O.S. and is quietly timing out.
I found the references in the MSKB on dual-booting with linux. Unfortunately, I don't remember the syntax, and am not particularly willing to look it up again.