I have to admit, I've never heard of Windows getting split over multiple HDD's.
The only thing I could think of, is that when resizing the partition, maybe your Windows files are larger than 10GB total. I imagine that would cause problems.
I would sugges manually editing the partitions during installation, not using the guided partition helper. A lot of times, it can end up doing things you didn't know it was doing.
How I set mine up.
Basicaly, I just resized my Windows NTFS partition.
Device Boot Start End Blocks Id System
/dev/sda1 * 1 16573 133122591 7 HPFS/NTFS
/dev/sda2 16574 23989 59569020 83 Linux
/dev/sda3 23990 24321 2666790 82 Linux swap / Solaris
And then created a Ext3 main partition, which is mounted to "/"
Then a swap of about 2GB, even though it never gets used.