I have encountered this problem the first time I repartitioned the drive too
I was really scared and wiped the drive. As I found out later I didnt have to... I think what you are experiencing is similar.
I used Partition Magic, but your software may support this too. Basically, the problem is that you cant' have more than 4 primary paritions. If you try to create more, some programs will "help out" and change the fs type of one of the partitions. To the program such a partition will appear as "hidden". To Windows it will appear to be garbage. Sometimes this change happens even with fewer than 4 partitions on the disk.
What can you do to fix this? In Partition Magic there is an option under "advanced" to "unhide" the partition. If you use some other program, there is probably something similar. If not, all you have to do is manually change the partition type in the partition table. There should be programs available for manual partition table editing.
This may also be a problem with your Grub configuration. It may help to take a look at the grub.conf file (it may also be called menu.lst).