need help recovering a partition

This is a weird problem but I hope someone can help me.

I had a PC with a windows XP installation.

It had two drives which were partitioned like this:

Disk 1, 1000 GB, 2 partitions

Disk 1, Part 1, 15 GB, windows XP system

Disk 1, Part 2, 985 GB, software

Disk2, 1000 GB, 2 partitions

Disk 2, Part 1, 500 GB, data

Disk 2, Part 2, 500 GB, data

This PC caught some virus which messed up the windows system.

I was planning on upgrading to new hardware and win7 so I didn't want to reinstall the windows XP system.

So I worked from a bootable Ubuntu usbstick for a short period.

From Ubuntu the partitions listed above were still there and perfectly accessible.

Using the partition editor tool that came with Ubuntu I rearranged the partitions and data.

Disk 1, 1000 GB, 1 partition

Disk 1, Part 1, 1000 GB, data

Disk2, 1000 GB, 1 partition

Disk 2, Part 1, 1000 GB, also data

I then added these disks to my new system, where I have installed windows 7.

Both disks where showing the partitions and data as I arranged it with Ubuntu.

I then started to copy the data from these disk to my new hard disk.

this went fine for disk 2 but somewhere near the end of the process for disk 1 it suddenly said that it could not find the data anymore.

When I checked in diskmanagement I say that the 1000 GB partition was gone.

Instead the original 15 GB and 985 GB partitions were back but they were not partitioned.

So my question are:

How did these two partitions suddenly come back?

How can I get the 1000 GB partition and the data on it back?

Thanks for any help you can offer.