Hi gmtyrant,

this is weird. Are you seeing any error message when launching the partitioning tool? Perhaps you could post your partition tables to see if it explains your problem.
Code:
# sfdisk -l /dev/hda > /tmp/sfdisk.out
# sfdisk -l /dev/hdc >> /tmp/sfdisk.out
This assumes two master IDE drives; you may need to adjust the device names. You can try the trusty cfdisk tool. Of course be careful on any disk where you want to preserve content (eg existing windows partition(s)). These are low-level commands that need to run as root, so type them from a text console (eg <Alt><F1> or prefix them with sudo). Also out of curiosity, give a look at the disk manager while under windows, and see if the partitions are displayed correctly there...