Well, I would say that the first thing that jumps out is the radically different Y axis on the four benchmarks for transfer rate ( one uses 200 MB/s, two use 150 MB/s, one is 90 MB/s ) consequently the amplitude delta of the transfer rate plots aren't good for fast visual comparison. It looks like this to me ...
SATA Western 2TB aux ... +/- 25 MB/s
SATA Samsung 2TB aux ... +/- 12 MB/s
SATA Samsung 2TB sys ... +/- 85 MB/s
.USB Samsung 500 aux ... +/- 08 MB/s
So they're tighter than they appear at first glance. If there was some way to use the same scale for all plots then a visual comparison would make some sense.
But then you clearly have the anomaly of that Samsung 2TB when it was a system disk. The temp was way higher at the time ( 11 degrees C and 20 degrees F higher ) and the dead giveaway of a bad benchmark was that minimum of 1.8 MB/s during that test. These should generally be thrown away and the test re-ran because outliers cause exactly this kind of discrepancy later when you look back to rate its performance in an earlier case. Most likely it was any number of Windows 7 services ( housecleaning, update check, event logging, RAM paging out, perf monitoring, registry flush, CEIP compiling or transmitting, file relocation, indexing, polling ). Polling occurs often because even though Windows "waits" for you to not be doing something to perform optional tasks and maintenance, it still has to cut in and determine if you are doing something ( kind of a paradox ). Just run ProcMon for a few seconds to get an idea of how many things are really going on. Of course any realtime antivirus will sour a benchmark in a variety of ways since it literally monitors everything you do. If there is any 3rd party software running ( anything from an open application to a Google, Bing, Java, Flash, Apple, HP, Norton or other updater services ) they can also pop in invisibly to make a quick update check or whatever. A lot of these events consist of reading a file that is isn't paged in memory from the disk, in order to see when the last update was, or whatever, and this might occur during the test and tank the benchmark maybe giving you that 1.8 MB/s. In this case the fact that the tested disk is also the system disk has a big penalty, but many of those things can affect an aux disk too.
Things I do to get smoother, comparable numbers. First of all know that the first three tabs in HDTune offer text copy/paste which I always dump into a text file ( naturally on the first tab you run the test first or you get blank results ). The data can later be added to a spreadsheet and you can do some math to get averages, min, max, whatever. This of course implies that you re-run the test multiple times and discard any outliers. Run the test after a reboot, but not immediately after reboot though. Give it a few minutes. And don't run it after sitting idle for a long period either.
When I make these HDTune text files I make sure they are identical format internally ( CRLF matching ) because I can then load a bunch of these separate files into a text editor and fast-switch between them for an A/B/C/... comparison ( think of how astronomers discover comets and asteroids using photos and ignoring stationary stars ). So any big changes jump right out of the data like temp, speed, SMART stats, etc. These are things you need to know. But of course this is dependent on first screening out bogus data due to Windows or some Windows program coming along and cutting in to your party.
I also run HDTach right before or after HDTune for a sanity check. If CPU is high on either, or the data differ by more than a few MB/s then I re-run them until they are very close.
It's a very imperfect Science, in fact I'd say it is closer to Art at this point in time. Windows isn't designed with any real modes for gaming, benchmarking, or even core maintenance. Nor does it accept a request to "back off and do nothing while I play this game or benchmark my computer". It should, but it doesn't ( and even if it did, it wouldn't prevent 3rd party apps or realtime AV from jumping in, often you can go in and disable the realtime AV or at least most of it ). So it makes sense to create an Administrator account where you go in and set it up for minimum distraction. Disable everything not needed and only benchmark from there ( leave the other user accounts set up for daily use ). It still isn't anywhere near perfect, especially on later versions of Windows, but you can get closer to the desired "Idle" state that is needed.
I also try to control the physical parameters as much as possible. The temps of the drives should match over time when they are still in the same physical location. Differences in temp means there is something that needs to be addressed. Most likely it is either dust build up, a fan is not running at the same speed or dead, a ribbon cable or something has altered airflow, or something far worse. I wouldn't proceed until I got the temp back to where it should be ( note: this does NOT describe your case here ). In your case I suspect the drive was in a different physical location when it was the system disk, perhaps vertically in the front bottom without a fan blowing on it, or mounted above something warm and warm air rose to affect it. I've seen them all.
What I have been doing for many years is collecting spare 3.5" cages out computer cases ( some hold two, four, even more drives ). I turn them into standalone HDD racks with rubber feet and a handle ( remove the sharp edges, paint them etc ) and modify my own cases by removing any HDD cages ( leaving a big empty space there ) add in 120mm fans in the front bottom. Now I just drop in one of the cages with HDD's already mounted and just pop in the wires already dangling off the motherboard and power supply. It makes drive swapping, cleaning and re-arrangement very quick and thorough and I can also easily get to the fans. Most importantly it means all my HDD's are always located in identical conditions on any computer with a fan blowing directly on it, no major vibrations ( rubber feet ). It is a consistently controlled parameter, well as much as possible. One of these days I'll post some pictures which will make it more understandable. The main point being, controlling variables that can make benchmarks anomalous and non-comparable. Of course this doesn't help if a benchmark occurred in the distant past and your time machine is broken, I have many historical cases that fall under that category and nothing can be done about it now ). But at least going forward all drives get the same treatment.