It would be better to read the boot sector directly, but I don't think Windows supports that. Another alternative is to use a boot sector file which finds and loads the real boot sector. This approach is used when loading Mac OS X or Darwin via chain0. You can obtain a version of chain0 at C:\NST\nst_mac.mbr by setting up a Mac OS X MBR boot entry in EasyBCD. The version I have has an MD5 value of cfca64f400ef99e89b51e59bcb697137. I patched it to search for the Linux partition instead of OS X and used that version as nst_linux.mbr:
C:\NST>fc /b nst_mac.mbr nst_linux.mbr
Comparing files nst_mac.mbr and NST_LINUX.MBR
0000008A: AB 83
00000090: A8 83
00000096: AF 83
It can search for three different partition types, but I only need to search for one so I set them all to 83 hex. This can successfully boot Linux from the first partition in my extended partition. If you have a more complicated setup, you may need a different version of chain0 with a fix for accessing other partitions in the extended partition.
Download the modified chain0 here.