Hi there
Get something like GPARTED -- bootable partition mamager and delete the partitions that way.
BTW Are you really sure you WANT to delete that partition. If you want to re-size partitions etc GPARTED also does that or simply take an image dump with say FREE MACRIUM. boot up GPARTED, re-arrange the partitions, then re-boot the FREE MACRIUM and restore your partitions to the new ones.
I don't think it's a good idea to have the boot partition in a logical partition. The boot partition is normally a small ACTIVE primary partition while the OS is in another PRIMARY partition.
Another way
1) delete with GPARTED the extended partition.
2) Insert the Windows install disk and choose recovery option.
3) it will now re-create a proper boot partition
4) re-boot your system.
Cheers
jimbo