found a solution, it was to use Device Manager to change Transfer Mode from "allow BIOS to determine transfer mode" to "DMA Mode".
For some reason that partition was transferring files a lot slower than the others and I guess the BIOS found a reason to use PIO mode.
Well I'm certainly confused.
You have to be very clear and unambiguous, when you refer to a "drive" vs. "partition" in describing a problem. They don't mean the same thing. Unfortunately Windows assigns a "drive letter" to a partition, so we kind of interchangeably and casually use drive, partition, even drive letter. But they're all very precisely different concepts, and using them improperly causes confusion.
You didn't post a screenshot from DISKMGMT.MSC, so we don't know exactly what your setup looks like. But it sounds like you have TWO physical drives.
One hard drive sounds like it's your primary drive where the C-partition lives, and it sounds like there's a second "data" partition on the same hard drive (I'll call it D).
The new SATA drive sounds like a second physical hard drive, and you have created three partitions on it (I'll letter them E, F, and G). One is a 1TB partition and the other two are 500GB partitions. Did you format all three partitions as NTFS when you created them? I'll assume yes.
If the BIOS (on your motherboard) has any setup option and therefore any effect on physical access to a physical hard drive, it would have that same effect on ALL PARTITIONS ON THAT HARD DRIVE. It cannot pick and choose how to support a specific partition on that drive.
On the other hand, if your two Casper backup/clone jobs have different setup options (relating to this BIOS vs. DMA mode option), maybe this is more likely responsible for the huge difference in job time. As was pointed out, writing to outer partitions on the drive is faster than writing to inner partitions (just because of the spinning speed at physical distances from the center of rotation), but that's a relatively minor difference that doesn't seem related to your story.
Just for closure here, can you please post a screenshot of your hard drive setup using DISKMGMT.MSC. Be sure to please maximize the window first, and also spread/separate the columns so that all text in each cell is visible and can be read, before you take your screenshot.
Thanks.