With my 3-2009 Seagate 500 GB sata hard drive, the re-allocated sectors count shows 2 bad sectors, in the Ubuntu 10.04 disk utility for the smart data. In this multi-boot desktop PC the XP with a drive monitor program called, Active Smart shows this drive health status as good.
Or can this be caused by mixed partitioning methods, since the new way is now align to MiB, and not align to cylinder as it was. I used the GParted tool to create and change partitions when it was set as default to align to cylinder, but then I recently used both my Vista Disk Manager, and the newer version of GParted to re-size some of the partitions, which both now use that align to MiB method by default.

It seems to be either
A, badblock on the hdd
B, bad cable

Best if you push badblocks through on it. If data does not needed then badblocks -w.
If you get badblocks on other computer too then throw away the drive, wouldnt worth risking your data.

Is there a wayto locate the bad sectors, and then attempt a repair ? Or are they now hidden bad sectors since they are now re-allocated ? If I do a file system check on all the partitions, will that find them, thanks.

Drives do that all the time. If you can find a low level format you may be able to see if it will clear up. They can be found because they are marked bad.

Okay then and thanks, also will having mixed partitioning methods cause any issues, since the new way is now align to MiB, and not align to cylinder as it was. I used the GParted tool to create and change partitions when it was set as default to align to cylinder, but then I recently used both my Vista Disk Manager, and the newer version of GParted to re-size some of the partitions, which both now use that align to MiB method by default. If I boot to that GParted tool, and change the default align setting to align to cylinder, then can I remove those 1 MB gaps by growing each respective partition to the right on that chart ?